So here's where I wish they would take what worked in Deception and Armegeddon conquest, mix it with some of the good of Shaolin Monks (spelled badly probably), and make a genuine action/adventure game set in the MK Universe. Let the official game's story mode be cinematic, but give us a way to explore the MK verse outside of the battle dramas too.
Probably never going to happen, but I'd have no problem with them reusing the character models in the main game(s) for something like that. If they do it right they could use it to do a more epic set up for the next main game that came after it too, rather than as a side story that happened years ago (compared to the current game), or as a sort of half-cannon exploitation of the massive ur-cast who aren't even in the main game.
They could even have another studio do the work, and I think it would be fine. If DC can make a good comic to go along with MK for once, I'm positive there's a studio known for adventure games that could do a spin off title justice.