While a Pokemon MMO sounds like an excellent idea, it would almost certainly do one or more of the following:
1: Be completely and utterly aimed at 7 year-olds. By which I mean overly simplistic, brightly coloured, easy...
2: Go for the "you are special" treatment...this may count as the above
3: Defeat the purpose of "legendary" Pokemon (ie how many Zapdoses can there really be?)
4: Be stuck on the Wii, which I don't think can really run an MMO.
As for other Pokemon 3D games, the traditional RPGs work best on handhelds. As do all good RPGs, really, imo.
The console games...Stadium was a fun multiplayer experience, Colosseum I have never played, and PBR is just a lazy excuse to make cheap money.