Less emphasis on becoming a Pokemon Master and more emphasis on what the player wants to be (Pokemon Trainer, Pokemon Breeder, Pokemon Coordinator, Item Creator/Seller, among many other possibilities. Maybe even opening up your own Gym?).
Customizable Characters (I think characters should start off with Basic clothing from a set which they can choose from and then have to buy new clothing. As for other things, people should be able to choose from many different hairstyles and hair colors as well as eye colors and facial hair for the guys. Also, actual customization of your characters frame (body shape) would be sweet too) with the ability to buy clothes as you make money and the ability to chance hairstyles/hair colors.
Character Profiles (this would keep track of your characters Win/Loss/Draw records as well as other things like that, but would also have room for lots of other information you could put in yourself, kinda like an MSN Profile).
just a few ideas i got alot more if ya would like to know.