I personally would like for game that feature choices (including Pokemon games) to have choices that directly impact the story. I know it's more time and coding, but it'll make it a more dynamic story. I read a article in some gaming blog that said that most games with the option for the player to choose things don't really affect the story much, you just get to the same result.
I would like to see a Pokemon game that's essentially a 'choose your own adventure' thing. The choices you make will make family members love or hate you more, will make bad guys reconsider their position on life, will drive your rival away for a short time, will make a gym leader quit, will make a girl/guy you save infatuated with you and want to follow you on your journey, will bring out your inner darkness, among many other possibilities. Having options that lead to these results will make a game more dynamic. Just a thought.