Miyamoto is helping with the development of Pokemon XD. Though, because of his close friendship to Satoshi Tajiri it's impossible to believe he has never had some input in the Pokemon games before.
He tends to do a little bit on most Nintendo first party games, often without much credit. Sometimes he's just there to give a good word of advice or something.
But, nothing has been confirmed about Miyamoto actually playing a real role in D/P's development and i'd highly doubt he'd have the time to have any real influence of a game that's going to be pretty much expertly covered under Tajiri's guidance.
And yes, mini-games are something D/P would be excessively empty without. Considering the amount of DS games that come with mini-games, i'd doubt D/P would be one to leave them out. They're often a great example of how you can use the touch screen and some games will probably confine a lot of their touch screen/DS functions simply to mini-games. Sonic Rush for example uses the D-pad and buttons for playing the main game, but mini-games are bound to use the touch screen in some capability too.