Needless to say, there's a lot of spoilers here. If you haven't beaten the game with all of the characters or played through the Story mode, then you should probably stop reading.
That being said, Story mode for the new Mortal Kombat game is a major clusterfuck. With the game basically setting itself up for a reboot of Mortal Kombat 4, nearly all of Earthrealm's warriors dead or really screwed up, you wonder who will be in the next game. So let's just get down to business.
First off, the ones that you can bet will be in the next game.
Shinnok - End game boss easy. I see him as a non-playable character as opposed to his first fighting game appearance (he originally appeared in Mythologies as the final boss) where he was both a playable character and the final boss. I imagine him having all of his old moves and some new ones to boot.
Quan Chi - Also easy. He caused all of the problems in the reboot. I know he will be in the next game.
Scorpion - Another easy one. He's a specter so you can't kill him and he's under Quan Chi's control. Also probably a fan favorite and the most popular character in the entire series.
Noob Saibot - Also a specter. Destroyed in the reboot after being sucked into the soulnado. Could be a bit difficult to explain, but hey, he's already dead. Can't get much worse off can he?
Sonya, Johnny Cage, Raiden - The only Earthrealm warriors to survive the Story mode. Probably some new looks for them plus new moves, but they're staples at this point.
Cyrax - Becomes a good guy in the original continuity. Captured by Sonya and reprogrammed to return his soul. Joins Special Forces. (OR according to his Ladder ending, becomes good and hangs out at the Shaolin Temple)
Sektor - Becomes the new grandmaster. Could be an enemy to Cyrax now.
Kano - After Cyber Sub-Zero's chapter in Story mode, he's never seen again so it's reasonable to assume he's still alive.
Sheeva - Also still alive, but her Ladder ending suggests she takes the Shokan to Earthrealm making her a possible Good alignment.
Mileena - Still alive, probably takes over Outworld in Shao Khan and Sindel's absence.
Reptile - Also still alive. Without Shao Khan and Shang Tsung around his allegiance is anyone's guess.
Baraka - Also alive and probably not doing anything since his character is more of a thug.
Ermac - Not only still around, but with Shao Khan dead his ladder ending could become his future. King Jerrod takes over his body and he joins Earthrealm.
Character that could possibly appear in the next game.
Liu Kang - Dies in Story mode at the hands of Raiden accidentally, could be resurrected. His (and Shang Tsung's) Ladder ending suggest he becomes a God to protect Earthrealm. He could easily be restored from the Elder Gods and takes Raiden's place with Raiden becoming mortal for killing him as punishment.
Smoke - Dies in Story mode, but his Ladder ending says he's part demon. No reason why he couldn't be resurrected.
Motaro - Killed by Raiden in Story mode. Safe to say he now resides in the Netherrealm thanks to Quan Chi's bargain with Shao Khan. Could be the secondary boss before Shinnok.
Mavado, Kobra, Kira, or Jarek - With Kabal dead (but Kano still alive), the Black Dragon might wonder what happened to him. I likely see Mavado, but Ed Boon didn't want any clone characters so Kobra is most likely since he isn't like any other character in the game.
Bo'Rai Cho - Seen in some of the Ladder endings, he could be involved finding out what happened to his student Liu Kang (or trying to stop him).
Tanya - Seen in Shao Khan's arena stage in early prototypes, she could make an appearance, but I wouldn't bet on it.
Havik - Very slim chance. He appears in Noob Saibot's Ladder ending, but that would suggest that Noob turned on Quan Chi which is unlikely.
Hotaru - Johnny Cage's Ladder ending could suggest him since Johnny suddenly has a problem with his powers. Still, I doubt Ed Boon is going to involve all of the other realms this early on.
Rain - A DLC character, his Ladder ending suggests he takes over Outworld so without Shao Khan around he could very well rule it.
Kenshi - Another DLC character. I doubt this some since his whole purpose is to defeat Shang Tsung and he was killed via transfer into Sindel to amplify her power. Without that, what is he going to do?
Skarlet - Third DLC, very strong that she returns, possibly even for Earthrealm. With Shao Khan dead because of the Netherrealm she might ally herself with them to get revenge.
Cyber-Subzero - Hard to say. He was killed by Sindel, but his ladder ending suggests he is possessed by Shao Khan's spirit. He could very well be in the next game with no real alignment at the time being.
Reiko, Frost, Taven, Daegon - All were either mentioned or seen at one time. Taven is unlikely since he was in hibernation as of the old continuity (things have changed though), Frost has no one to train her since Sub-Zero is no longer around in the same way, Reiko and Daegon seem the most likely since Reiko is mentioned in Story mode and Daegon can be seen fighting on the Pit stage (he is also active according to MK: Armageddon)
Characters not coming back most likely.
Kitana, Jade, Stryker, Jax, Kabal, Nightwolf, Sindel, Kung Lao, and Shang Tsung - All killed by either Shao Khan or Sindel at some point in Story mode.
Kratos and Freddy Krueger - These are characters from entirely different franchises. I feel that these guys were one-offs.
So, barring they don't decide to just bring everyone back (possibly evil since they are under Quan Chi's control), here's what I perceive provides the most realistic roster.
Roster: Quan Chi, Ermac, Sonya Blade, Johnny Cage, Raiden, Scorpion, Noob Saibot, Cyber Sub-Zero, Rain, Reptile, Baraka, Sheeva, Skarlet, Bo'Rai Cho, Mileena, Reiko, Liu Kang, Cyrax, Sektor, Mavado.
Add in a few DLC: Tanya, Daegon, Nitara, Zombie versions of dead characters, etc.
Seems like a great start. Of course, like with Cyber Sub-Zero and Skarlet, the MK team might just make a few new characters we have never seen.