Well, I would like to see changes in the contests. They get kinda' annoying in Ruby, Sapphire, and Emerald when you have a really high score and you are just about to win, and then one of the other contestants "scares" your Pokemon into losing points and the contest. I think it should be more like in the TV show, you practice, maybe in a Pokemon Center or something, then you appeal in the contest, then you battle it out. It might take longer, but it would interest me more.
And about the mini games, maybe there would be seperate contests for medals or money or something. You would find someone somewhere and then choose a Pokemon and a mini game. There could be restrictions (wieght, type, height etc.) too.