Interesting idea. Normally I would question how popular a Pokemon MMO with no Pokemon could be, but if Pokemon Online was successful then maybe... hmm. It'd be tricky to get around copyright violations - remember the fake Pokemon Game Boy games? - but it might be worth it While I must admit I question the addition of new types, the possibilities that a Fakemon MMO opens are fascinating. (3-way battles = awesome!)
Of course, the primary problem with a fan-made MMO is getting a dedicated team. I suppose it could be done in Flash, at least in the beginning; depending on how vast the RPG were to get it might eventually require a more advanced language.