Umm I would like to see Kung Lao turn evil. His jealosy of Liu Kang turns him against his former allies.

Kung Lao's never been jealous of Liu Kang...except for Shaolin Monks which was non-canon.
Regarding alignment shifts...
Mileena should go neutral. She should let go of her hatred for Kitana and realize it's Shao Kahn's fault her life sucks, which makes her change. She shouldn't go completely good, but not evil anymore.
Frost should keep going evil. I guess one could say she already is, but I don't want her to have some sort of repentence in her Unchained ending and be a good guy in Armageddon. She should join with Noob Saibot against Sub-Zero.
Jax should turn evil. He should not recover from Onaga's corruption. Could add some depth to his character and lead to an interesting situation with Sonya.
Raiden should shift towards evil. His anger and impatience grows and soon he blames the Elder Gods for what's happening as well and tries to take his own power.
I think Reptile should go neutral or good. Similar to Mileena, he finally realize show much Shao Kahn's screwed him his whole life. Maybe offering his service to Edenia's forces or just going solo.
Nitara should turn evil. She's currently considered neutral, but I'd like to see her and the Vampires become a future threat.
Sareena should stay neutral, but lean towards the good side...if not be good all together. I think it'd be better and more interesting for her story than being evil.
That's all I can really think of now.