Alright here is what I'm thinking.
Some sort of new enemy appears, but is an enemy to both the villains and the heroes.
The Villains and Heroes are still able to damage/fight eachother.
Although they can fight eachother, this will make defeating the enemy harder to accomplish. They really won't be able to defeat this common enemy without working together. (Maybe certain things that Heroes can do that Villains can't and vice versa)
All Targeting done with the mouse, so you don't accidently click someone.
Maybe afterwords you have the option of switching sides.
This would allow for some cool new temp powers/new areas to explore.
There has to be some point where the player has to choose the route they will take, but overall its going to either help the big picture or hurt it.
I'm not sure what the enemy would be, but I was just thinking about this last night. Waddaya think? Any Ideas/comments?