What I would like:
Ability to start off in Kanto, win the 8badges and such, Elite 4, then go to Johto.
Johto (same in Kanto), progress, then you go to Hoenn. After that, you go to Shinou.
They should make the boy in the game more like Ash, the dimwits they choose are such LOSERS!
THey're not even SEEN in the show itself so make the boy character like Ash.
Have more team ups, like in Kanto, have your character team up with Claire to stop Team ROcket and other team ups.
Make the contests similar to what you see on the TV, it doesn't seem right to have 2 versions in game, then TV tells a different story about it. Have them in each region, but you can have it in one arena for all 4 events.
Team up with Pokemon Ranger.