While you can say that MKvDC/MK9/Injustice uses Unreal Engine 3, it's far from a correct answer honestly. There has been so much done to their in-house Unreal 3 BASED engine that you can't just call it that and be done with it. Almost every developer has done extensive rework to make Unreal Engine 3 do what they want to do, and the "NetherRealm engine" is no exception. The differences this creates makes almost none of these engines cross-compatible.
Either way, what engines the game uses won't make a MK vs SF crossover game any easier or harder. The hardest thing is that Capcom and Warner Bros. are two different companies. Working together on a project like this is rare, and after the lack of success of SF x Tekken and the possible cancellation of Tekken x SF due to low sales means that a MK x SF is less likely.
Also doesn't help that various fighting game developers get along just as well as the communities of the games they create do.