So I saw a kick ass signature of Sonya that someone has from MK VS DC when she gets a power ring. I have never been in LOVE with Sonya, but she has kept my interest and she's interesting. I'd almost like it if she was somehow evil in this reality.
Characters I'd like to see go to the other side
NOW BAD
Sonya
Kitana
Sindel (stay evil)
Jade
Goro (stay evil)
NOW GOOD
Noob Saibot (if he is even going to exist)
Smoke
Cyrax (good from the start with no need for a rebooted system, if he is even a cyborg at all)
Ermac
Tanya
Rain
For the Edenian side I think this would add a new direction. Having Queen Sindel and Princess Kitana evil along side Shao Kahn (OR A LIVING KING JERROD) and Tanya as part of some kind of resistance force against them. Have Jade play a similar role but be a double agent. Evil but REALLY working for the side of good with Tanya.
I've always been a sucker for the Edenian Realm and would like to see it be the focus again along with Earth realm focusing on SubZero and Scorpion and the (maybe are or not) Cyber Ninja's and leave the stupid Black and Red Dragons out of it, or as a lesser plot line.