Piggybacking on this point: I'm not seeing a convincing reason for the "really" rebellious/evil/amoral guys to take instructions from the Dark Lord who enlisted them. For example, would Lex Luthor be satisfied to see her defeat Superman for him, or would he rather stay in his original universe to do it himself? I am simplifying this a lot and it is dependent on character choice and game suitability, but from the perspective of a player with some villainous characters I'm not finding any distinctive difference between this and other "you can do anything if you support the mighty NPCs, NPCs give you benefits" settings.