Here are a couple of ideas for MK. Usually in the games they make great characters/stories but then they scrap them after. If you think about it many of the "new characters" for each game were not in future games. When I say this MKU3 and MKT do not count.

In MK4 they had Quan-Chi, Fujin, Tanya, Jarek, Shinnok, Reiko and Kai for new characters and out of them all only Quan-Chi returned. So on with my ideas:

DRAHMIN & QUAN-CHI
I think that they should fuse together and this results in Drahmin returning to normal but he has Quan-Chi's spirit fighting for control. He would have Quan-Chi's styles and you could unlock Quan-Chi or something with a code. He could take over his body after Drahmin died and returns to his normal state.

VAMPIRES
Nitara may be not be in MK6 but it might be cool if her race would ivade the Outworld after being set free. Think how cool a battle arena would be to see hundreds of vampires fighting above.

FORGOTTEN CHARACTERS
Maybe, if they keep the Krypt, you could unlock a bonus video or story about what happened to other characters like with Baraka in DA. Maybe show the fight between Kabal and Mavado, Reiko's future or a battle between Outworld and Zaterra.