There are a number of unresolved characters and characters who survived, as well as characters not formally introduced into story mode:
Unresolved:
Sektor
Cyrax
Noob Saibot (Bi-Han)
Shinnok (teased at the end of MK9)
Survived:
Raiden (In)
Johnny Cage
Sonya
Scorpion (In)
Ermac (In)
Reptile (In)
Mileena (Teased in comic)
Kano (In)
Baraka
Sheeva
Quan-Chi (In)
Goro (In)
Kintaro
Not Directly Involved in Main Story: (so assumed to be alive)
Kenshi (Teased in comic)
Skarlet
Rain
Dead:
Sub-Zero (Kuai-Liang)
Liu Kang
Kung Lao (In)
Sindel
Kitana (In)
Jade
Nightwolf
Smoke
Jax
Stryker
Shang Tsung
Kabal
Shao Kahn
Ok, so lets start with the Netherrealm war:
I'm speculating that it's actually between Quan-Chi and Shinnok.
-Quan Chi gives Shinnok a duplicate of his amulet, keeping the original for himself.
I believe this war was over who will rule the NR, however, it may also have to do with the amulet. This could also get Onaga involved because:
-The amulet was once held by Onaga, who has an innate power to raise the dead. This could explain the return of resurrected characters.
-Quan is controlling the "dead" characters' souls, I guess that explains the zombie look in that scene in MK9. With the return of Kung Lao, he somehow was resurrected and his soul freed. This leads me to believe that Quan did NOT resurrect. Shinnok or Onaga maybe?
Character speculation:
Sub-Zero:
When playing against Scorpion:
Scorpion: Murderer...
Sub-Zero: I tire of maintaining our innocence.
Scorpion: I will relieve you of your burden!
This leads me to believe that Sub is either Bi-Han or a new Sub. The line "I Tire of maintaining our innocence", to me, implies that "our" refers to the LK and the vision shown to Scorpion by Quan in MK9 of the LK slaughtering his clan and family. In MK9, Bi-Han says to Scorpion that it was not him that did it. We know through numerous storylines that it was always Quan who did it. By saying "I Tire", it implies to Scorpion "This is getting old already". Lastly... no scar. Sub is either Bi-Han or a new Sub, but my guess is that the Soulnado, just like it had done to Scorpion in the past, ripped Bi-Han out of Noob. If noob exists anymore, I don't know, but I think SZ is Bi-Han.
I'm still at work. If anyone wants me to do more speculation, let me know and I'll do my best.