Miyamoto is right, some games just don't work on 3D, and some don't work on 2D... Mario is one that works both ways (but is more popular in 2D)...
I was thinking about what someone posted about Pokemon in 3D, and the game can work with some good cel-shading, full 360 view for exploration, and when a Wild Pokemon is found, switch to a battle screen with the old system and anime-esque scenes...