I wonder if they ever did make an MMO for Pokemon, would we care about it? I usually don't play spin-off games that don't aid the Pokemon in my regular games, but if I could use the Pokemon I've worked hard on already towards this game then it might be cool.
Maybe if it were just some online tournament game with a nifty lobby area. The lobby area of Dead or Alive 4 comes to mind where people ran around looking for fights or chatting, with a funky custom hat and a favorite Pokemon in tow.
I think the simplest direction a Pokemon MMO would take is just simply dropping everyone into the same game of Pokemon. It would probably end up like the DS games, but random encounters would probably be replaced with wandering Pokemon, and then we'd probably see a few million tournaments for anything you could imagine. Type specific tournaments, contests, etc.
The first problem with an MMO though is that it would create a separate world from the DS games. No one would want people importing DS pokemon into an MMO because of the fear of hacks. And as the DS games get updated generation to generation, expansion packs would be required to be released at the same time to keep the Pokemon catalog up to date in both game worlds.
The biggest reason Nintendo won't do this: Competition. Pokemon is all about battling, and Nintendo clearly dislikes having good players beat the crap out of the bad ones (see Brawl getting dumbed down, blue shells, etc), which is exactly what would happen in this MMOs environment. All the serious battlers would be winning whatever tournaments that pop up, and all the people that carry six Butterfree because it looks cool would be crying about how unfair the world is.
If Nintendo does get around to making a Pokemon MMO, its likely to be a shitty spin off or they're going to further rape the game mechanics of the game with more random number generators.