The processes for breeding and EV training your Pokemon has changed drastically with the arrival of Gen VI, making both far easier and far more accessible for all players. While these processes may seem daunting for new players, once you get used to them they become second-nature, and you can breed and train all kinds of strong Pokemon with ease. Before we go into the processes behind how to breed and train Pokemon, it's important to know exactly what you're looking for to know whether or not your Pokemon is as strong as it can be. For this guide, we will be detailing what you need to know about breeding Pokemon and how to do it.
POKEMON NATURES
The first notable aspect of breeding are Pokemon Natures. Every Pokemon has a nature, such as Docile, Timid, Rash etc. on their stats, and each nature with the exception of five which do absolutely nothing (Docile, Bashful, Serious, Quirky and Hardy) will increase one of your stats by 10% while reducing another by 10%. Having the right natures on your Pokemon is key to maximizing their potential. For example, every fast sweeper or disruptor such as Greninja or Thundurus will want a speed-boosting nature to maximize their greatest strength and ensure they can get their moves off before the opponent can, assuming you run max Speed EVs on both too – more on that later. A Pokemon focused on defensive strategies will likely want a nature that boosts whichever defense it needs more focus on, such as Skarmory wanting a Defense-boosting nature to maximize its physical durability, and even Blissey potentially going for the same in order to cushion its greatest weakness since its special defensive abilities are already very potent unboosted. Note however that these natures also lower a stat by 10%, and typically you want the lowered stat to be one that you'll likely never have use for anyway. Going back to the previous examples, Skarmory's Sp.Attack is terrible, and as such Skarmory has no use for special attacks at all; therefore Impish is a brilliant nature for Skarmory as it boosts its greatest stat (Defense) and lowers a stat you have no use for anyway (Sp.Attack.) As for Greninja, if he's running a mixed set, say for example Ice Beam/Low Kick/Gunk Shot/Dark Pulse, he'll still want a Speed-boosting nature but now all of his stats have some kind of use. In this case, you're probably better off going for a Hasty nature, boosting Greninja's speed while lowering physical defense, as that is his lowest stat anyway and decreasing it further is likely to have the least negative impact on his effectiveness. With practice you'll learn exactly which natures are best in which situations and for which Pokemon. For a list of all the Pokemon natures and what they do to your stats, check this Bulbapedia page:
http://bulbapedia.bulbagarden.net/wiki/Nature
Of course, knowing which natures are best isn't enough alone – you need to know how to get these natures onto the correct Pokemon. Luckily breeding for Pokemon natures is the easy part; when two Pokemon are put into Day Care, if one of them is holding the Everstone item, then any Pokemon bred from the two will have the same nature as the Everstone holder. So, all you have to do is get a compatible Pokemon with the nature that you're looking for, give it an Everstone and pop it into Day Care and there you go – nature breeding in a nutshell.
INDIVIDUAL VALUES (IVs)
That's the easy bit – IV breeding is the hard part. First of all, what are they? IVs, or Individual Values, are hidden numbers every Pokemon has, they are decided the moment the Pokemon is spawned into the game either as an egg or as a wild Pokemon and cannot ever be changed. Every Pokemon has one IV per stat, and each IV can be any value between 0 and 31. Put simply, the higher each IV is, the higher its respective stat will be, so naturally in the vast majority of cases you'll want an IV of 31 in every stat. There are some exceptions to this rule, such as when breeding for specific Hidden Power types, but for now we will focus simply on how to get a perfect IV spread on your Pokemon.
HOW TO BREED THE PERFECT POKEMON
First of all you need to get some Pokemon that have 31 IVs in one or more of their stats. Now since IVs are completely random this can sound like a horrendous ordeal, however Gen VI has provided some relatively easy methods for getting hold of Pokemon that are guaranteed to have 31 IVs in some of their stats. The first and most notable method is the Friend Safari; every Pokemon you catch in the Friend Safari is guaranteed a 31 IV in two of their stats, chosen at random, so by catching a bunch of Pokemon from the Friend Safari you can get yourself a collection of Pokemon with 31 IVs that you can then use to breed their IVs onto your chosen Pokemon. Also, any Pokemon that cannot breed is guaranteed to have three 31 IVs in its stat spread, again chosen at random. While this may seem pointless to suggest since, well, the Pokemon can't breed, this includes baby Pokemon – which can evolve into Pokemon that CAN breed, such as wild Pichu evolving into Pikachu that can be bred. Catching some baby Pokemon and evolving them can give you a larger stock of 31 IVs to breed across to the Pokemon you want to use in battle.
So, now you have Pokemon with 31 IVs in some stats – now you need to use those Pokemon to breed new Pokemon that have 31 IVs in all of their stats. Now unfortunately getting 31 IVs in every stat is still extremely difficult, however getting 31 IVs in five stats is a lot more manageable, and usually five is all you need (Alakazam won't care about his Attack IV for example.) So from this point on we'll be explaining the breeding process in full.
First things first – when breeding two Pokemon of different species, the female's species is the one that is carried over to the eggs. If you're new to breeding Pokemon this is worth keeping in mind as we progress. So, for example's sake, we're going to breed ourselves a special attacking Froakie with the hidden ability Protean. We have a Rash natured, male Froakie, a Timid Ditto, and a male Azurill whose nature is not relevant. The Froakie is from the Friend Safari, so it has a 31 IV in Defense and Speed, and it also has Protean. Azurill was caught in the wild, and since it's a baby Pokemon it has 31 IV in Defense, Sp. Attack and Sp.Defense. Ditto has no 31 IVs at all in this example, however for special attacking Greninja Timid is the best nature to use, and as stated our Froakie is male, so we need a female Timid Froakie with Protean to breed with our Azurill. So, the first step will be breeding our Froakie with our Ditto.
I'm going to try and condense the rest of the process down to prevent it from becoming too wordy, so here we go. Give Ditto the Everstone mentioned earlier so that its Timid nature is passed onto its babies first off, but there's one other item we need: Destiny Knot, which we will give to Froakie. This item increases the number of IVs the parents transfer to their children when breeding, which we definitely will need. It doesn't matter which parent carries this item, so it can be given to whichever isn't holding the Everstone. So:
Male 31 IV Defense/Speed Rash Protean Froakie (Destiny Knot)
+
Timid Ditto (Everstone)
=
Female 31 IV Speed Timid Protean Froakie
Keep in mind that the breeding process is still fairly random, so all the steps will be hypothetical examples, so here we have ended up with our female Froakie, correct ability and nature, but we lost the Defense 31 IV in the transition. Not perfect, but since Azurill has a 31 Defense IV as stated earlier, we don't need it. Of note as well: Normally only female Pokemon can breed hidden abilities across to their children, but if the other parent is Ditto, then the hidden ability can be passed on by male or female Pokemon. Next we evolve Azurill into Marill and hatch a bunch more eggs until we eventually get:
Female 31 IV Speed Timid Protean Froakie (Everstone)
+
Male 31 IV Defense/Sp.Atk/Sp.Def Marill (Destiny Knot)
=
Female 31 IV Defense/Sp.Atk/Speed Timid Protean Froakie
Another female Froakie, but this one has more perfect IVs than our old one. So what we do here is swap the old Froakie for this new one, and continue the process. Since it has more perfect IVs and some of those IVs overlap with the Marill, there's more chance that between the two parents those perfect IVs will be passed onto the children, thus speeding up the process. So eventually:
Female 31 IV Defense/Sp.Atk/Speed Timid Protean Froakie (Everstone)
+
Male 31 IV Defense/Sp.Atk/Sp.Def Marill (Destiny Knot)
=
Male 31 IV Defense/Sp.Atk/Sp.Def/Speed Timid Froakie
We now have a male Froakie with four perfect IVs. Note that having two Pokemon of the same species breeding with each other will increase the rate at which they spawn eggs, plus we now have another 31 IV for the male Pokemon side – also a bonus. The male's nature (which will also be Timid anyway) and ability do not matter for now, as the female is holding the Everstone and is the only one here that can transfer the Protean ability anyway. So we'll be replacing Marill with our new male Froakie, giving it the Destiny Knot. However, despite our success, we've been missing one key thing throughout the entire process so far: a 31 IV in HP.
Back to the Friend Safari – we need a female Protean Froakie with a 31 IV in HP. We catch one with Adamant nature, 31 in HP and Sp.Attack and swap it for our previous female Froakie – even though it has one less perfect IV than the previous female, between it and the male we just bred we now have a 31 IV in every stat we need between the two parents. Since the male has four perfect IVs out of five, we will never need to swap him out from this point onwards. Moving on:
Female 31 IV HP/Sp.Atk Adamant Protean Froakie (Destiny Knot)
+
Male 31 IV Defense/Sp.Atk/Sp.Def/Speed Timid Froakie (Everstone)
=
Female 31 IV HP/Defense/Sp.Def/Speed Timid Protean Froakie
Note that we've swapped the Everstone onto the male Froakie now, as the female no longer has the correct nature. The female will now be swapped out for the new one we just got, and from this point onwards we won't need to swap out either of our two Froakie as both of them have four out of five perfect IVs and between them they have the five that we want, so the final step will be:
Female 31 IV HP/Defense/Sp.Def/Speed Timid Protean Froakie (Destiny Knot)
+
Male 31 IV Defense/Sp.Atk/Sp.Def/Speed Timid Froakie (Everstone)
=
Male 31 IV HP/Defense/Sp.Atk/Sp.Def/Speed Timid Protean Froakie
And there you have it. From a total of four Pokemon we caught in the wild, we've managed to make a perfect Pokemon via the breeding process. While it may be a bit long-winded and arduous since a lot of the breeding process is determined by the game's random number generator being kind to you, this process is the easiest and quickest way to get the job done. Long story short: catch some Pokemon with perfect IVs, start breeding, and gradually swap each of the parent Pokemon for new ones you've bred with more perfect IVs than the previous ones until you eventually get a Pokemon hatching with a perfect IV spread. It's worth noting that the more Pokemon you breed, the easier this process gradually becomes, as you'll eventually end up with a bunch of perfect Pokemon that you can then use to help breed others by passing their perfect IVs onto your new Pokemon.
ADDITIONAL NOTES
A few other things I'll gloss over to wrap this up: Having a Pokemon in your party with the abilities Flame Body or Magma Armour will halve the amount of time it takes to hatch the eggs. In Gen VI Talonflame is by far the best Pokemon for the job as it also gets Fly, allowing you to fly between Day Care and the IV stat checker, who can be found in Kiloude City Pokemon Centre in X/Y and the Battle Resort Pokemon Centre in OR/AS. The IV stat checker is how you find out where each Pokemon's perfect IVs are; if you have a 31 IV in any stat, he will point out which stats have 31 IVs in them and say that those stats “simply can't be beat,” so thanks to him it's very easy to find out which Pokemon have the IVs you're looking for.
That's the hardest aspect of breeding dealt with outside of Hidden Power, which is a whole other kettle of fish that I won't be detailing here since odds are if you're breeding for specific Hidden Power types you probably don't need to be reading a breeding guide anyway. Other aspects of breeding include egg moves, which are moves that Pokemon can only learn by being bred with something else carrying the move(s) in question, but breeding them onto your Pokemon is as simple as having one of the parents (usually the male, but as of Gen VI both parents can transfer egg moves) carry the move you wish to breed onto the Pokemon.
POKEMON NATURES
The first notable aspect of breeding are Pokemon Natures. Every Pokemon has a nature, such as Docile, Timid, Rash etc. on their stats, and each nature with the exception of five which do absolutely nothing (Docile, Bashful, Serious, Quirky and Hardy) will increase one of your stats by 10% while reducing another by 10%. Having the right natures on your Pokemon is key to maximizing their potential. For example, every fast sweeper or disruptor such as Greninja or Thundurus will want a speed-boosting nature to maximize their greatest strength and ensure they can get their moves off before the opponent can, assuming you run max Speed EVs on both too – more on that later. A Pokemon focused on defensive strategies will likely want a nature that boosts whichever defense it needs more focus on, such as Skarmory wanting a Defense-boosting nature to maximize its physical durability, and even Blissey potentially going for the same in order to cushion its greatest weakness since its special defensive abilities are already very potent unboosted. Note however that these natures also lower a stat by 10%, and typically you want the lowered stat to be one that you'll likely never have use for anyway. Going back to the previous examples, Skarmory's Sp.Attack is terrible, and as such Skarmory has no use for special attacks at all; therefore Impish is a brilliant nature for Skarmory as it boosts its greatest stat (Defense) and lowers a stat you have no use for anyway (Sp.Attack.) As for Greninja, if he's running a mixed set, say for example Ice Beam/Low Kick/Gunk Shot/Dark Pulse, he'll still want a Speed-boosting nature but now all of his stats have some kind of use. In this case, you're probably better off going for a Hasty nature, boosting Greninja's speed while lowering physical defense, as that is his lowest stat anyway and decreasing it further is likely to have the least negative impact on his effectiveness. With practice you'll learn exactly which natures are best in which situations and for which Pokemon. For a list of all the Pokemon natures and what they do to your stats, check this Bulbapedia page:
http://bulbapedia.bulbagarden.net/wiki/Nature
Of course, knowing which natures are best isn't enough alone – you need to know how to get these natures onto the correct Pokemon. Luckily breeding for Pokemon natures is the easy part; when two Pokemon are put into Day Care, if one of them is holding the Everstone item, then any Pokemon bred from the two will have the same nature as the Everstone holder. So, all you have to do is get a compatible Pokemon with the nature that you're looking for, give it an Everstone and pop it into Day Care and there you go – nature breeding in a nutshell.
INDIVIDUAL VALUES (IVs)
That's the easy bit – IV breeding is the hard part. First of all, what are they? IVs, or Individual Values, are hidden numbers every Pokemon has, they are decided the moment the Pokemon is spawned into the game either as an egg or as a wild Pokemon and cannot ever be changed. Every Pokemon has one IV per stat, and each IV can be any value between 0 and 31. Put simply, the higher each IV is, the higher its respective stat will be, so naturally in the vast majority of cases you'll want an IV of 31 in every stat. There are some exceptions to this rule, such as when breeding for specific Hidden Power types, but for now we will focus simply on how to get a perfect IV spread on your Pokemon.
HOW TO BREED THE PERFECT POKEMON
First of all you need to get some Pokemon that have 31 IVs in one or more of their stats. Now since IVs are completely random this can sound like a horrendous ordeal, however Gen VI has provided some relatively easy methods for getting hold of Pokemon that are guaranteed to have 31 IVs in some of their stats. The first and most notable method is the Friend Safari; every Pokemon you catch in the Friend Safari is guaranteed a 31 IV in two of their stats, chosen at random, so by catching a bunch of Pokemon from the Friend Safari you can get yourself a collection of Pokemon with 31 IVs that you can then use to breed their IVs onto your chosen Pokemon. Also, any Pokemon that cannot breed is guaranteed to have three 31 IVs in its stat spread, again chosen at random. While this may seem pointless to suggest since, well, the Pokemon can't breed, this includes baby Pokemon – which can evolve into Pokemon that CAN breed, such as wild Pichu evolving into Pikachu that can be bred. Catching some baby Pokemon and evolving them can give you a larger stock of 31 IVs to breed across to the Pokemon you want to use in battle.
So, now you have Pokemon with 31 IVs in some stats – now you need to use those Pokemon to breed new Pokemon that have 31 IVs in all of their stats. Now unfortunately getting 31 IVs in every stat is still extremely difficult, however getting 31 IVs in five stats is a lot more manageable, and usually five is all you need (Alakazam won't care about his Attack IV for example.) So from this point on we'll be explaining the breeding process in full.
First things first – when breeding two Pokemon of different species, the female's species is the one that is carried over to the eggs. If you're new to breeding Pokemon this is worth keeping in mind as we progress. So, for example's sake, we're going to breed ourselves a special attacking Froakie with the hidden ability Protean. We have a Rash natured, male Froakie, a Timid Ditto, and a male Azurill whose nature is not relevant. The Froakie is from the Friend Safari, so it has a 31 IV in Defense and Speed, and it also has Protean. Azurill was caught in the wild, and since it's a baby Pokemon it has 31 IV in Defense, Sp. Attack and Sp.Defense. Ditto has no 31 IVs at all in this example, however for special attacking Greninja Timid is the best nature to use, and as stated our Froakie is male, so we need a female Timid Froakie with Protean to breed with our Azurill. So, the first step will be breeding our Froakie with our Ditto.
I'm going to try and condense the rest of the process down to prevent it from becoming too wordy, so here we go. Give Ditto the Everstone mentioned earlier so that its Timid nature is passed onto its babies first off, but there's one other item we need: Destiny Knot, which we will give to Froakie. This item increases the number of IVs the parents transfer to their children when breeding, which we definitely will need. It doesn't matter which parent carries this item, so it can be given to whichever isn't holding the Everstone. So:
Male 31 IV Defense/Speed Rash Protean Froakie (Destiny Knot)
+
Timid Ditto (Everstone)
=
Female 31 IV Speed Timid Protean Froakie
Keep in mind that the breeding process is still fairly random, so all the steps will be hypothetical examples, so here we have ended up with our female Froakie, correct ability and nature, but we lost the Defense 31 IV in the transition. Not perfect, but since Azurill has a 31 Defense IV as stated earlier, we don't need it. Of note as well: Normally only female Pokemon can breed hidden abilities across to their children, but if the other parent is Ditto, then the hidden ability can be passed on by male or female Pokemon. Next we evolve Azurill into Marill and hatch a bunch more eggs until we eventually get:
Female 31 IV Speed Timid Protean Froakie (Everstone)
+
Male 31 IV Defense/Sp.Atk/Sp.Def Marill (Destiny Knot)
=
Female 31 IV Defense/Sp.Atk/Speed Timid Protean Froakie
Another female Froakie, but this one has more perfect IVs than our old one. So what we do here is swap the old Froakie for this new one, and continue the process. Since it has more perfect IVs and some of those IVs overlap with the Marill, there's more chance that between the two parents those perfect IVs will be passed onto the children, thus speeding up the process. So eventually:
Female 31 IV Defense/Sp.Atk/Speed Timid Protean Froakie (Everstone)
+
Male 31 IV Defense/Sp.Atk/Sp.Def Marill (Destiny Knot)
=
Male 31 IV Defense/Sp.Atk/Sp.Def/Speed Timid Froakie
We now have a male Froakie with four perfect IVs. Note that having two Pokemon of the same species breeding with each other will increase the rate at which they spawn eggs, plus we now have another 31 IV for the male Pokemon side – also a bonus. The male's nature (which will also be Timid anyway) and ability do not matter for now, as the female is holding the Everstone and is the only one here that can transfer the Protean ability anyway. So we'll be replacing Marill with our new male Froakie, giving it the Destiny Knot. However, despite our success, we've been missing one key thing throughout the entire process so far: a 31 IV in HP.
Back to the Friend Safari – we need a female Protean Froakie with a 31 IV in HP. We catch one with Adamant nature, 31 in HP and Sp.Attack and swap it for our previous female Froakie – even though it has one less perfect IV than the previous female, between it and the male we just bred we now have a 31 IV in every stat we need between the two parents. Since the male has four perfect IVs out of five, we will never need to swap him out from this point onwards. Moving on:
Female 31 IV HP/Sp.Atk Adamant Protean Froakie (Destiny Knot)
+
Male 31 IV Defense/Sp.Atk/Sp.Def/Speed Timid Froakie (Everstone)
=
Female 31 IV HP/Defense/Sp.Def/Speed Timid Protean Froakie
Note that we've swapped the Everstone onto the male Froakie now, as the female no longer has the correct nature. The female will now be swapped out for the new one we just got, and from this point onwards we won't need to swap out either of our two Froakie as both of them have four out of five perfect IVs and between them they have the five that we want, so the final step will be:
Female 31 IV HP/Defense/Sp.Def/Speed Timid Protean Froakie (Destiny Knot)
+
Male 31 IV Defense/Sp.Atk/Sp.Def/Speed Timid Froakie (Everstone)
=
Male 31 IV HP/Defense/Sp.Atk/Sp.Def/Speed Timid Protean Froakie
And there you have it. From a total of four Pokemon we caught in the wild, we've managed to make a perfect Pokemon via the breeding process. While it may be a bit long-winded and arduous since a lot of the breeding process is determined by the game's random number generator being kind to you, this process is the easiest and quickest way to get the job done. Long story short: catch some Pokemon with perfect IVs, start breeding, and gradually swap each of the parent Pokemon for new ones you've bred with more perfect IVs than the previous ones until you eventually get a Pokemon hatching with a perfect IV spread. It's worth noting that the more Pokemon you breed, the easier this process gradually becomes, as you'll eventually end up with a bunch of perfect Pokemon that you can then use to help breed others by passing their perfect IVs onto your new Pokemon.
ADDITIONAL NOTES
A few other things I'll gloss over to wrap this up: Having a Pokemon in your party with the abilities Flame Body or Magma Armour will halve the amount of time it takes to hatch the eggs. In Gen VI Talonflame is by far the best Pokemon for the job as it also gets Fly, allowing you to fly between Day Care and the IV stat checker, who can be found in Kiloude City Pokemon Centre in X/Y and the Battle Resort Pokemon Centre in OR/AS. The IV stat checker is how you find out where each Pokemon's perfect IVs are; if you have a 31 IV in any stat, he will point out which stats have 31 IVs in them and say that those stats “simply can't be beat,” so thanks to him it's very easy to find out which Pokemon have the IVs you're looking for.
That's the hardest aspect of breeding dealt with outside of Hidden Power, which is a whole other kettle of fish that I won't be detailing here since odds are if you're breeding for specific Hidden Power types you probably don't need to be reading a breeding guide anyway. Other aspects of breeding include egg moves, which are moves that Pokemon can only learn by being bred with something else carrying the move(s) in question, but breeding them onto your Pokemon is as simple as having one of the parents (usually the male, but as of Gen VI both parents can transfer egg moves) carry the move you wish to breed onto the Pokemon.