How would you set up the MMO premise for Marvel?
Make this an alternate Earth where Scarlet Witch never turned into Crossover Queen. The world still has thousands of mutants, and governments around the world are desperate to find ways to cope with this explosion of powered entities.
New players can create a mutant, or a tech/training character from one of the many programs set up to deal with mutants. Other origins (magic, cosmic rays, etc) would be unlockable or added in expansions. Mutants would start off with one power and learn new ways to use it as they gain experience. At some point, they'd unlock a Secondary Mutation. Tech characters would have access to various relatively mundane gear (think SHIELD agent grunts, so maybe jetpacks as the high end), and instead of a Secondary Mutation they'd get to pick up a more advanced tech path (powered armor being an obvious possibility). Both archetypes would have access to training abilities (martial arts, mental resistance techniques, etc), although the tech characters might get better versions.