What if one of the elder beings that presides over all universes mashes both universes together to see which one is strongest. But people from both sides join the other so we'd get something like Batman, Wolverine, Deadshot versus Green Arrow, Cyclops (x-men), and Doomsday? Then one of the other beings, because there are a ton of them, thinks the first one has done wrong by meddling with the universes and thus creates a new set of heroes to send down and stop the war. This'd only work with original characters but it'd be interesting to see a three way war with having to possible take on famous superheroes/villains. I'm not sure what else the group would be working towards besides just mindlessly beating up on people though...