I've done some thinking about a new Mortal Kombat game, as I really enjoyed the main MK story arc and thought there were places to go after Armageddon. I felt that the story of Armageddon was quite forced, but that an aftermath was completely salvageable. I think that I would like to return to that storyline with a two game arc. In the first game, I would have the main story be an uprising from the Netherrealm, now controlled by Noob Saibot, who has overthrown Shinnok and has essentially become a "Shadow God." It will be hard to limit myself to 12 returning characters, but here are the ones that I feel would be most pressing to this main storyline:
1. Sub-Zero
The younger brother to Noob Saibot, and last we saw he was becoming more powerful with his ice capabilities, almost to the point where he was an "Ice God" in his own right. He's also seen his allies fall to darkness a lot, and he would take responsibility for that and fight against The Brotherhood that is now threatening the realms.
2. Scorpion
The man who killed Noob Saibot, and almost his antithesis. He's also one of the most popular characters, and love him or hate him, you can't really take him out of the story. It just so happens that he would fit perfectly fighting alongside Sub-Zero to battle the entity he was instrumental in creating.
3. Sareena
A character that "never really got a chance," but still has an extremely loyal bunch of followers. Her story would be most compelling, because on hand she admired the original Sub-Zero, but his falling into darkness would make it easy for her to concede her own dark nature. Or would this younger Sub-Zero, not the same man she fell for, continue to inspire the good in her? Her choices would make her an absolutely compelling character to follow.
4. Ashrah
A great character concept that seemed so "pure," but in her purity was a misguidance and a tunnel-vision that was almost militant. Her steadfastness in her decisions to slay evil would make her a great counterpoint to Sareena and her confusion. I think the battle between these two would be at the centre to their stories.
5. Smoke
Never one of my favorite characters, but I have to concede his popularity and there is no better time to include him in a main MK storyline than in a collision between his former best friend and his new master. Returning as a mixture between a cybernetic ninja and a wraith, Smoke would provide a challenging obstacle for Sub-Zero to battle en route to facing his brother.
6. Frost
Another odd choice, but in this storyline, I think she would fit like a warm glove -- the "warm" of course being an ironic choice of wording. Sub-Zero's prized pupil who wanted to take power for herself and fell into darkness. Killed by Sub-Zero in Armageddon, she returns having sold her soul to Noob Saibot, the darker brother she could have followed. Her character would be modified to reflect the darkness inside her, and she could use a combination of shadow and ice specials which could separate her more from her stigma of being "the female Sub-Zero."
7. Raiden
He's one of those characters that you just can't seem to remove from the story lines without upsetting people. He's become a part of Mortal Kombat and it's just a matter of making him fit. In a story about hell rising up and mortals trying to snatch the powers of gods, Raiden would make an obvious choice to stand against Noob Saibot and his attempt and gaining control of the realm of the living. They recently tried to give Raiden a darker side, and it was interesting, but I think after nearly becoming desensitised to mortality, Raiden can pull himself back from the edge after a battle with Liu Kang, Kung Lao and Kai in Armageddon, where he is reminded of their valiance. Raiden once again fights on the side of humanity.
8. Kung Lao
I thought the time for him to become the main protagonist sailed with him losing in Deadly Alliance, but the character's popularity and familiarity to gamers cannot be denied. After a battle with Raiden, Kung Lao is wounded and loses an arm. Despite offers from Sonya and Earth's Special Forces to give him a technological replacement, Kung Lao decides to remain one-armed as a reminder of the darkness that almost overcame Raiden. Lao continues to fight, but using only one arm would certainly make him an intriguing and "battle tested" character to fight against the Brotherhood of the Shadow.
9. Kitana
She and Sonya are the iconic MK females, so it would make complete sense to include them in a sequel to Mortal Kombat. Armageddon would see Kitana finally overcome certain obstacles that have been plaguing her existence since her introduction to the series -- she kills her sister and Shao Kahn. After Armageddon, I'd have her mother the victim of an assassination, leaving Kitana to rule Edenia as Queen, evolving her character into one with even more responsibility and no one to turn to. A darker and more broodish Kitana, who realises that there are some people who do not want to see the former assassin of their oppressor rule the realm. Perhaps Kitana can find herself the obsession of a new character who has had someone close to them killed by Kitana for attempting to lead an early rebellion against Shao Kahn? The sins of Kitana's past haunting her as she heads into an unsure future would make her character quite the interesting one.
10. Sonya
I'm not her biggest fan, but she's very recognisable and that does the series a good service. She's a sturdy protagonist and one that could have her own conflicts coming out of Armageddon, having lost many of her closest friends and allies (or so she thinks). In Armageddon, I'd have had Cyrax and Jax kidnapped by Sektor and his Tekunin, and written off as dead by Sonya. Jax, however, would have escaped and destroyed the Tekunin base from within, closing up Sektor's story. Jax, having felt abandoned by Sonya after constantly following her across realms to save her life, would become warped by the experience, and go renegade and want Sonya to pay for her betrayal. Evil Jax would certainly freshen up him as a character, wouldn't it?
11. Jax
So that brings me to the big man himself. Again, not my favourite character, but another one that seems to be pretty close to the core of what makes Mortal Kombat the series that it is. Perhaps Sektor may have started some cybernetic experiments on him, causing certain empathic qualities Jax may have possessed to have disappeared. Losing sight of any patriotic desire to do what is right, all he wants to do now is crush Sonya's pretty little skull.
12. Havik
This is where I get more subjective. There are other characters that I think would have fit the storyline a whole lot better -- Nightwolf, Jade, Mileena (now loyal to Noob Saibot and more animal than ever) Kenshi, Kano, Mavado, Taven, and Li Mei are all other characters I would bring back in this game as well -- but since I'm going to have to stop at 12, I'm going to put Havik here, because I feel as if he could become an icon of Mortal Kombat himself. The chaotic figure that just wants to cause anarchy wherever he goes. He doesn't care who he fights, or even why, he would always provide a trigger for some bad event happening. As a character who sits outside the main story and is just there to do cool moves and wicked Fatalities, Havik has a "purity" to him that I think is too valuable to leave in the stories of MK past.
If I could keep going, the list would go to 19 characters. Many of them would see this as a swan song, providing obstacles for other characters to kill (again) and close up certain chapters of their development. This story would see the destruction of Noob Saibot and a seeming return to order of the realms, setting that stage for a more classic threat to the MK realms -- a foreign ruler trying to come in using a bunch of new warriors to fight against the surviving protagonists. This game would introduce a few of them (a female sorcerer and her bodyguard with an honourable warrior past who now wields the War Hammer of Shao Kahn he discovers upon arriving in Outworld) and even introduce some potential allies to fight against them (a darkly armoured berzerker who wields retractable twin blades, almost like Zorro crossed with Baraka). Then you also have that new character who was behind the death of Sindel and is now attempting to kill Kitana due to their past as allies to Shao Kahn (a personal vendetta more than anything). I'd probably make her a female character just because it seems to fit.
That'd take my main roster of Mortal Kombat X (which would be a cool name for the game, even if I have lost track of just what true number this would be chronologically) to 24 characters, which fits nicely on a grid of 8 x 3 or 6 x 4.
big thanks to flameshang for the sig. 
