As a mod, when I'm organizing my cast list, I have a few different designations for the marvel pups.
The Marvel Cinematic Universe is actually it's own self-titled canon, something that's already been dealt with here in the comics.
When we've got movie versions of x-men, we call that "Movieverse" at my game.
This is because - as has been pointed out - these universes don't actually cohabitate. You will never hear talk of Wolverine in any Iron Man or Avenger's movie, nor can Spider man or the FF exist there. Because of this, lumping them all together doesn't seem consistent, but I think it widely depends on the kind of game you're running.
Mine is a lot based on the idea that these fictional universes actually exist and can be visited, so the designation is really important there.