I agree with the second option and the weather moves should take effect out of battle, like in pokemon ranger or something. Or an ability! I also wish that the accesories could be used in battle as well. And I hope the poketch is much better than DPPt
....DONT DO IT! THE CAKE IS A LIE! Thanks to Keshavkd........YAY Awesomeness....
My wishlist: RPG stats for the trainer as well. Could be taken as an aggregate of all the pokemon ex points. Trainer ex points could be used to improve stuff like catch probability, walking speed, EV gains.etc
Isometric viewpoint. Aaghh we need that. What's the point of a 3d game then? (with non-combatable pokemon flying in the environment.cool)
HM-replacing items. Pleasepleaseplease. This could be given once the trainer completes the e4/side quests. Something like STRENGTH gloves or DEFOG fan. :[
Special multiplayer dungeons. Somwhat like Zelda 4 swords. These need not be vital to the game but may be required to gain certain special items/TMs etc. NPCs are morons compared to the fun you could have with an actual human. And human interactivity should be beyond union rooms/underground.
This is wishing too much, but a programmable auto-engage system, somewhat like Dragon Age, would be awesome. The only trade-off would be that the trainer would get reduced evs/less chances of finding a legend.