Hmm...I'm not really sure where to start here - there's nothing I generally dislike about the Pokemon games that has been consistent with all four generations, so I'll go for what I disliked most about each one individually:
Gen I: Hmm...my main issue with Gen I (which they did fix for Gen II luckily) was the player's bag. At the end of the day, having all your items in just one slot was a complete mess, and this was something that I noticed very quickly when playing through Pokemon Red for the first time. Another issue was with the Psychic-type imbalance which was not only absolutely ridiculous in terms of gameplay, but also because the anime itself had said that Psychic-types were weak to Ghost-types, and in the games it was the exact opposite - Ghost-type moves, bar Night Shade, did 0 damage to Psychic-types, and the Ghosts would suffer super effective damage from the Psychics due to their secondary Poison-type.
Gen II: My main grudge with Gen II, to be honest, is with the internal battery dying as it stands right now, but since that doesn't really count I'm going to overlook it for this. There isn't really anything I greatly disliked about Gen II, aside from the Kanto Gym Leaders, and pretty much the whole of Kanto in general, felt like it was just tagged on the give the game extra longevity. Hell, you couldn't even see the Kanto Leaders' badges on the player status menu, which just goes to show how significant the developers considered that part of the game. Kanto needed a lot more work done on it, since it made for a very disappointing conclusion to an otherwise amazing generation.
Gen III: The downgraded time function was a major disappointment for me as far as Gen III was concerned, as it was a major step backwards from what Gen II provided in that area. My main issue with Gen III however comes from its difficulty, or lack thereof - Groudon and Kyogre are capable of completely devastating the Elite Four by themselves, and Emerald lets you grab a lv 70 Rayquaza before facing the Elite Four. Put simply, there was nothing "elite" about the Elite Four in R/S/E, unless you hadn't bothered catching Groudon/Kyogre/Rayquaza beforehand, and even then they weren't any harder than the Elite Four from the previous generations.
FR/LG removed the internal clock completely - this I did not like at all, especially after what R/S/E did with the internal clock. Now granted, the clock didn't exist in Gen I, but that's no reason to remove it completely here, especially since FR/LG were clearly quite different from the originals in Gen I anyway, and deliberately so.
Colosseum and XD made up for Gen III's general lack of difficulty, however I did not like the way Colosseum practically forced you to grind your levels up if you had more than 2 team members, since that isn't adding to the difficulty in a good way, that's adding to it in a lazy and tedious way. XD made up for it by being considerably kinder than Colosseum whilst providing a good challenge nonetheless.
Gen IV: Gen IV was a major step in the right direction from Gen III - it was a much better challenge, the internal clock was back again, and it just generally looked like more care had gone into its development. However, my biggest grudge with Diamond/Pearl is the abysmally slow Surf speed - who in the world thought that this was a good idea? Evidenly, that person was fired prior to Platinum's release, since the Surf speed was returned to normal in Platinum.
My second problem is the absurd amount of legendaries. Heatran was a pointless addition, and so was Shaymin - neither of them have any real role besides wasting space in the Pokedex, especially since in Shaymin's case, Manaphy was already there as the "cute" legendary...which brings me onto Phione, which is the most useless waste of space in the entire Pokedex. Phione did not need to exist at all, especially since it effectively exists to be ignored in favour of Manaphy.
Finally, something that RLRL touched on, is the stupidity of Battle Tower's hax. Whether it be Focus Band triggering twice in a row, horrendous abuse of Double Team, an insane number of Wobbuffets and general Quick Claw/BrightPowder stupidity, Battle Tower is just plain ridiculous. I wouldn't mind if this happened only occasionally, but this happens ALL THE TIME. Again, this just comes down to the developers being lazy with the challenge of the game as far as I'm concerned. I don't care that much about hax, but relying on it as much as Battle Tower does is just ridiculous.
My main complaints with Battle Revolution is that the Stadium games were better than it was, due to them allowing you to do more within the game (battling in-game characters, mini-games etc.) Also, Battle Rev. is guilty of using Double Team all the time, just like Battle Tower - if they've put in Sleep Clause, would it have killed them to stick Evasion Clause in the game too? Next, both Neon Colosseum and Sunset Colosseum are vile, with each relying on pure luck and pure hax respectively, and with the amount of hax the CPUs get on Sunset Colosseum, I get the feeling that "Sunhax Colosseum" would have been a far more appropriate name for it. Just to wrap it all up...why does Battle Rev. Wi-Fi permit the use of Ubers? Battle Tower forbids them, why doesn't Battle Revolution? Overall, Battle Rev. seemed very rushed, and it's obvious that very little care went into its development.
