I think there would be more than enough to cover a Pokemon MMO. You're right that it wouldn't be a traditional MMO, but it would certainly be an MMORPG I'd play with lots to do:

You mentioned the different species/races/skills etc; It would be amazing to explore because there are four regions, it would work out well if you could choose which region you wanted to start out with - regions could be the 'faction' (loosely speaking in MMO terms), and there could be special event days where you could take a cruise to the other regions and catch Pokemon that aren't in your island. And through Pokemon technology, even if you didn't make the cruise in-time, if you have a friend in another region you could trade?

The regions are also quite big, bearing in mind they would be towns and cities, not the 1/4 scale you get from the portable games. Exploration would be rife and plentiful! Seek the strongest, rarest Pokemon in the top of the mountain? There could be customisation/aesthetics that certain people would like -customising their own PokeTrainer/avatar, Secret Bases, the various types of Pokemon Contests, Pokeball customisation. For a completest there is so much because of all the items needed/required.

And PVP.. haha, c'mon! PVP would of course be Pokebattles! If you could see other players about like a normal MMO, you could request a duel right there and then! Competitions!

Quests? : To be the very best. (And occasionally run an errand for your region's professor.. OH, AND BEAT TEAM ROCKET/PLASMA/AQUA/MAGMA/WHATEVERTHEFUCKTHEYCALLTHEMSELVES.)

...Yes, I've always dreamed of a Pokemon MMO.