Well this makes me think to Metin2 or similar games, where the balance of the game is based on a mixed team with different roles. This is not a bad idea but would completely change game and this won't be a Pokemon based game anymore.
Hunters would be involved in only hunting sessions, PvPers into battle ones, and as said in other comments, "Pokemon Trainer" is the best role someone can have, since you can do everything.
Imagine if we promote this suggestion and make roles real, wouldn't people ask for being Pokemon Trainers one day and not only PvPers for example? Also we should consider that some people love to get involved in more than one "profession".
I would honestly play a game made as you suggested, but that won't be a Pokemon Based MMO in that case ^^