Dead: Jade, Jax, Kabal, Kitana, Kung Lao, Motaro, Nightwolf, Noob Saibot (Bi Han), Shang Tsung, Sindel, Smoke, Stryker.
Returning/Revived/Fixed:Cyber Sub-Zero (alternate costume in ladder: Human Sub-Zero), Robo-Smoke (Sektor could collect his body at the temple and turn him into his cyborg form - Alternate costume: Human Smoke).
Big boss: Onaga & Shinnok (story/character depending: the final boss could be different in ladder kombat).
Sub-Bosses: Daegon, Blaze & Moloch.
Story (more or less):
After Shao Kahn's defeat, Outworld is led by Onaga (the intro can be placed around his emergence) followed by the Tarkatans & the Shokan (Goro, Kintaro and Sheeva make a comeback). Reptile, Mileena, Rain, Sektor and the Lin Kuei still enforce Outworld. Kano, Kobra, Kira & Jarek ally with Outworld as well.
As a result, Mavado and Hsu Hao (though I could live without Hsu Hao’s homosexual costume) is on NetherRealm's side. Outworld's last stand comes to a halt as Shinnok and his minions take over Outworld. We could possibly see how ruthless & powerful Shinnok really is by killing off a bunch of outworld characters during Part1 (during which the player can control some of the popular, "bad" NetherRealm guys such as Quan Chi, Reiko, Daegon and Mavado).
Shinnok followed by Daegon, Reiko, Quan Chi, Drahmin, Moloch, Tanya, Mavado, Hsu Hao, Havik, Darrius, Dairou, Ashrah and Nitara (Sareena possibly?) plus any possible Outworld survivors and now comrades (Reptile?), leads the attack against Earthrealm. I would have a good 30-40% of Outworlds cast serve Shinnok after Outworld’s defeat.
Kobra, Kira, Jarek, some of the Shokan (Goro is the favorite to stay alive) and Mileena are expendable in my opinion, meaning they could be dead after Shinnok’s attack. Then the next part could take place and evolve around EarthRealm’s defenses lead by the new protector of Earthrealm, Liu Kang while Fujin is the Elder Gods’ messenger to observe and consult the rookie Kang. Raiden is turned into a mortal with amazing powers (that’s my story twist concerning the good guys). Kang is not dead but seriously injured in the finale of MK9's story mode and later his request for a one match mortal kombat is granted by the elder gods etc...
Kang is deformed (Kabal-like) and has a back and forth relationship with Raiden while Fujin is there to stabilize things when they get out of hand. We could see an enigmatic Kang being powerful (as his MK9 ending suggested) but lacking the discipline and wisdom that Raiden had as Earthrealm’s protector. Maybe even killing one of the good guys in a show of anger and aggression near MK10's story mode, THEN having him realize that he is just not ready for such a heavy burden and having Fujin and Raiden taking over near the end.
Cage, Sonya, Cyber Sub-Zero, Frost, Cyrax, Kai, Fujin, Raiden, Ermac (King Jerrod-he;s a good guy now, free of Kahn's spell), Bo Rai Cho, Hotaru, Kenshi, Taven, Shujinko and Li Mei enforce Earth’s “good guys”. Tanya could work as “double agent”/traitor during story mode on behalf of NetherRealm’s side meaning, she could be the reason for some of the good guys’ cast dying in a treacherous plot.
Ideas people?...