I would like to see Defog given a more useful ability. Its just far to common to be useless. If I could change it I would say, make it a PP of 5 and give it the ability to clear all weather conditions. There are alot of PKMN out there that run weather effects, this could be the counter.
Separate field effects from moves. Allow each pokemon to have like two or three slots for field moves, some of the side games have. There's lots to do as far as side quest and I hate HM slaves. Also there's a good chance that the next game will alot more online content a la Ragnarok Online, not the whole game mind you.
I would also like the ability to change Pokeballs. I would love it if I could buy new Pokeballs and put my Pokemon in them. Example, I breed a new Staryu, he comes in a standard red/white ball. I would equip a Diveball on him. The old Pokeball would be destroyed (to keep people from reusing Masterballs) and Staryu would find itself in a nice new Diveball. I think this is a reasonable request as we now can see the Pokeballs used in the DS game as well as PBR. I feel it would give a touch of customization to trainers, especially people like me who run mono or theme parties.
Allow the ability to have some/all/none of your pokemon follow you.
I want to be able to select which pokemon goes first using my touch screen, instead of being determined by who's first in party.
A better Water/Dark type then the two we have.
If this thing comes out on the next gen system, and there's room, allow me to travel to all the regions.
More underwater routes.
That's all I have so far