I don't mean beating up players, man. I mean the equivalent of a fox hunt run by a staffer, with a somewhat moderated outcome, decided by the event staffer. In a simulated environment, would you rather chase down a rabbit on a rail, or would you rather play paintball?
I just get the image of the Riddler and some outmanned goons being beaten up by Batman whenever I think about the idea of a comic book PvE MUSH enters my mind.
Besides, it's hell on event staff. The real problem is that comic books don't have defined factions in the source canon, and that's the entire carbuncle that a MUSH formula works on. So you'd have to make a few, not even the 'groups' standard, but actual organized units that stick true to the MUSH's canon inspiration. Two heroic, one villain, one support hero, is what I'd advise. Design the alternate character policy around the number and your prospective playerbase draw goal.