I've always wanted to see an RPG-style game where you start as a lowly character and then rise to power, only for it to be revealed that you are Shao Kahn. Then they made him a god or something, so I'm not sure how I feel about that idea now.
A popular one is a Kitana, Mileena and Jade action game. That one makes a lot of sense. The same goes for Sub-Zero and Scorpion.
I was listening to Netherkast's The Lost podcast on characters (strong recommend), and in their Kung Lao retrospective Razor mentioned Kung Lao possibly being trapped in Outworld after the defeat of Shao Kahn in MK3, explaining his solitude until MK Gold. This is a bit of a retcon, but I would have Kung Lao defeated by Shao Kahn in MK3 and trapped in Outworld after Kahn is defeated, but then he recovers and needs to fight his way back to Earthrealm. Outworld is such a zany place. Kung Lao can maybe even be hunting Goro during this period, learning that he has returned to lead the Shokan against the centaurs. Lao also learns about the survival of Shao Kahn in this game, and when he ambushes Goro while he is conferencing with Kitana, it is him that informs them that Kahn still lives, which leads to the events of Deadly Alliance.