Maybe I've been watching too much wrestling, but I think it'd be interesting if a shadow faction emerged from within the two waring "good" and "evil" factions. Like for example, somewhere in the midst Kano, Kung Lao, Goro, and Jade formed an alliance to take over EarthRealm, Outworld, the Netherrealm, and Edenia....they saw through the good vs. evil nonsense and realized that if they came together as one force, they could both end the war by defeating both side, and conquer all of the realms (so there would be a good, and not so good reason for it), but it would catch both sides completely off guard and the good and evil warriors would have to put aside their differences to battle this new threat.
I've always been a fan of the angle of a shadow third party that kind of gets hinted at but you don't know who it is, and some of the people turn out to be your allies. I think that would be an extremely interesting plot twist.
And it doesn't have to be those 4 I named, or even limited to 4 (could be 3, could be 5, 6, or whatever). Any combination of good and evil warriors that would make sense and you could build a story around I think would be a great plot twist for the next game (and something that would be an awesome ending for this one).
It would be Deadly Alliance taken to the next level. Deadly Alliance was great, but it was still two super evil guys. What if DA had been Liu Kang teaming up with Shang Tsung instead of Quan Chi? Every being has a dark side, even Liu Kang, no matter how small it is. Imagine Shang being able to tap into that somehow (telling him that if they conquered the realms together, he would finally be able to have his revenge on the murderers of the White Lotus).
I think finding a way to bring Shang and Liu closer to common ground (both giving a little from their good/evil tendencies, to become more neutral) would have made a much more dynamic story and pairing for end bosses in that game.
That's the kind of ground that I think could take Mortal Kombat to another level story wise, but that's also the kind of ground Boon probably will never tread on.