I think MUA was a test for this game. You'll probablly have different "rooms" or "communities", and in each seperate room the Marvel roster is selectable. Everyone from Hawkeye to The Sentry. And that way there won't be any clones because if every character is taken, then the room will be "full".
Or it could be one huge world and each city would represent a "room". So if you're spidey in LA. You can't go to NY, because someone is playing spidey there. OR if you're in latveria, maybe there's a spidey in europe so you can't go there.
I don't see why they don't just let players pick who they want and then explain it as some kind of time parodoxing dimensional rip.