Funny enough, I've always held Pokémon to be the perfect intersection between a massively multiplayer game and an alternate-reality game. After you've completed the main quest, the endgame is you roaming the in-game world and collecting pokémon, while meeting people in the real world and having your in-game worlds interact by battling each other, trading pokémon and more, in the newer games.

I think an actual Pokémon MMORPG just wouldn't be the same really.