Let's do the math.
(This is a long read, by the way, you may need a snack.)
Already Back In:
Scorpion, Sub-Zero, Raiden.
Definitely Still Alive:
Kintaro, Goro, Shinnok, Quan Chi, Baraka, Cyrax, Ermac, Johnny Cage, Kano, Kenshi, Mileena, Reptile, Rain, Sektor, Sheeva, Skarlet, Sonya Blade.
Definitely Dead At This Particular Moment:
Jax, Jade, Kabal, Kitana, Kung Lao, Liu Kang, Nightwolf, Shang Tsung, Sindel, Smoke, Stryker.
Up For Debate:
Noob Saibot.
Now, any and all hypotheses that could be rendered at this point, however convoluted or mind-blowing they may be, are made completely and utterly circumstantial until we get more info about the impending new story/how it's going to coexist with the mythos of old, due to one simple fact: Sub-Zero is already in rotation. Which means that potentially anyone, alive or dead, could have the door opened to slip back in for their piece of the pie. But it would still be easy enough to build the new story while still keeping the old one intact.
In my opinion...this is what I would see as my ideal outcome, not counting any eventual DLC, and assuming that the aforementioned math is right and there will only be 8 of the original MK9 lineup returning (which if we're looking at 14 new characters and a total starting roster of 30 leaves 8 spaces for anyone from the MK4-MKA timeline to be woven in) :
-Shinnok gets in. That's a given. That's one for the New 8, makes it 3-1.
-I expect this mass of new story direction to give a lot of left-out characters room to contribute to the tale in some important manner or another.
-Pick one of the next-gen characters for every realm of the Six, since each one had what I guess you'd call a top character out of the newer cast members, like someone who was most important to that particular place. Fujin, Ashrah, Havik, Bo Rai Cho, Hotaru, Tanya. That's seven altogether. And for number 8, you add in the one guy destined to travel them all: Shujinko. There's your new-gen 8, all of whom played the most significant roles out of everyone during that particular run of games.
-If we're still planning to cement on top of said run of games, there are only two people on the entire list of the dead or missing that play any irreplaceably significant role in the story that couldn't be filtered into backstory or cutscene ammunition: Liu Kang and Sindel.
-Liu's demise is what set the entire Deadly Alliance angle into motion; almost everything that happened throughout was an effect stemming from him being double teamed and dispatched. They brought the motherfucker back from the dead just to give him a shot at zombie revenge. The way he was disposed of in MK9, literally having to sit there and watch your most revered and trusted protector doom all of mankind and bring about the death of every person you cared for, and then have to die (and end up imprisoned by Quan Chi, because remember, the deal he made with Khan says EVERYONE who dies in the conflict is his to enslave, so he's already Quan's to start) with all of that on your conscience and not get to live to see Raiden turn out to be right...I'm making the easy call and saying Kang gets back in as your new cutthroat villain, and that Quan Chi doesn't get in because his creation kills his creator, steals his power, and teams up with Shinnok to bring about Deadly Alliance Ver. 2.
-Sindel gets back in simply because Edenia's going to need a leader, I don't see any of the other ladies being revived over her, and her "oh god what have I done" face turn would make for great cinematics and better story. That's five out of eight.
-The Baraka VS Mileena storyline I predict is going to be turned into story fodder so as to leave them both out since they're too busy trying to destroy each other.
-Johnny Cage and Sonya Blade having a kid that encompasses both of their styles leaves having either pointless.
-Kano I think is gonna get the wrong end of karma and get turned into a Dragon by Daegon like he was supposed to in MKA.
-I cannot for the life of me envision a way Sheeva gets in.
(That leaves 4 originals and 3 DLC: Kenshi, Reptile, Rain, Sektor, Skarlet, Cyrax, and Ermac.)
-Ermac gets in. He's the only character out of the pile with a really important part to play in getting control of his own being, which will likely lead to Kenshi being relegated to his story mode sidekick, since Shang Tsung staying dead undoes his only important task to accomplish throughout the 3D storyline.
-Reptile gets in because he's fucking Reptile, and I think if they turned him into Onaga again, it'd make for a really interesting Oni boss.
-I'm completely torn on who gets the last spot. Any on the 4 of them could make for a great addition, especially with the implementation of the 3 styles. Sektor could invade with the Tekunin horde, Rain could overthrow Tanya and Sindel or whoever's in charge and lead a revolt, Cyrax could go all good guy zen and restore order to the Lin Kuei...but I think all three of them (especially Cyrax given how much chaos he caused in MK9's metagame) are going to be left aside in favor or giving Skarlet room to be expanded on and explored.
So...if the new character total is 14, that leaves this as my Top 16:
Returning From MK9: Scorpion, Sub-Zero, Raiden, Reptile, Ermac, Liu Kang, Sindel, Skarlet.
Returning from MK4-MKA: Shinnok, Fujin, Ashrah, Havik, Bo Rai Cho, Hotaru, Tanya, Shujinko.
/Theory.
