MegaMan Star Force is a prime example of why 3D models would be a bad idea.
3D Environments: Good
3D models: Bad
Only problem. If you see gen V, the sprites look awful and out of place with the rest of the world.
The main complaints about the last games by reviewers, were that the battle system was old and outdated. Same with the graphics and sound.
If pokemon did become 3d, then I would want it to look better then PBR. If they used new models, they can do it, but if they keep using the n64 models (Like in HGSS for cutscenes and the title screen), then it would not be good. And it would SUCK if they used the wiiware models. Or they could make it like that pokemon arcade game, where it is all cel shaded.