I'd definitely play a Mutant Academy game ala what you'd described with the X-Men. Even from that brief synopsis of what the setting might consist of, I can see a lot of potential there. Especially if you selected certain points in the X-Men time-line - I'm thinking around issue 200ish of Uncanny X-Men.
There's lots of opportunities there with the New Mutants cross-overs or even some Alpha Flight thrown in for our friends up north.

In the meantime, Phoenix was doing her phoenix thing, and Kurt decided it was a good idea to scamper off to England with Beast for some wacky Excalibur adventures.
Mind you all of those things would be more about providing a solid setting to play in - players themselves would be students still learning how to use their powers, with opportunities cropping up that would allow them to join the bad guys if they wanted etc.
But beyond that, I agree - it would be really hard to pull off an MMO if the focus were on a single hero setting. For example, I'd love to see a Marshal Law game, but it would be just as hard to pull off as a Batman-centric title for a lot of the same reasons. Plus, ML had a very short run so there's a lot less lore to draw from.
Out of curiosity, do you think that kind of focused content might work for an expansion once a broader setting is already established (as with DC Universe)?