Forget a Pokemon MMO. How about instead we first test the waters with an actual 3D RPG. Wouldn't happen though because Game Freaks and Nintendo refuse to innovate.
The closest thing I can think of to a 3D Pokemon RPG is the child-gambler game they have at the arcade where you have your child put in some cash, they spot a pokemon, and then they wail on a tiny button until it is caught. If they win, they get more cash.