Ed specifically said: "It's going to be a fun surprise returning character. Some people, not a lot of people will see it coming, but there's a lot of surprises in the story."
Going with that, yes, it shouldn't be Shao Kahn and it also shouldn't be Shang Tsung, but I can't rule them out completely.
Shinnok is more probable, but... and this is a very important but... how popular and known is he? Not to us, but the average mainstream casual audience/players. On a scale of 1 to 10. 4? 6? More?
The thing is, it has to be (or should be) a popular character people know. Not us, but people. The character has to be fun (could be anyone) and his return should surprise people.
Would Shinnok as the main boss surprise people or would they see it coming? We all suspect he's in the game, at least as a boss/sub-boss, but that's us - hardcore fans that know their stuff back and forth even at 3am. But what about Joe Average?
This factor alone eliminates many of the potential candidates. Everybody knows Shao Kahn and Shang Tsung by now. Everybody. So I doubt their return would surprise anyone. Plus they've been done to death and this game is supposed to be about the NEW.
So that brings us back to Shinnok, who story-wise makes sense. Heck, I think he's a given. But... is he bad enough?
Same for Quan-Chi. Obviously he's bad as well, but again... bad enough?
Together? Perhaps. Alone? I simply don't think so. Which brings us to Liu Kang.
Why him? Putting aside he's probably the most recognized and known MK character that has been basically in every game, getting also his own game and being the main hero of the movies, his MK9 ending is all one needs to see.
Liu became a god, the new protector of Earthrealm. Raiden is no more. He basically created the Fantastic Four and is who knows where.
And with Raiden out of the way, it will also be Fujin's moment to shine.
The thing is, though, that Liu is pretty angry right now. He's not a happy god. He's a pissed god.
But as Ermac says, he is but one. He needs help.
So who's he gonna call? Shinnok and Quan Chi of course. The evil duo. Or maybe they'll call him.
Either way they make a deal of some sort and decide to help each other and cooperate. Or maybe Quan Chi will totally brainwash Liu to make things easier.
Quan Chi and Shinnok will be sub-bosses and Dark Kang will be the main boss at the very end.
Makes perfect sense to me.
It can't be anyone else than Liu Kang, because no one else will shock the mainstream audience. Everybody thinks all these years that Liu is the good guy. The hero. The chosen one. He's been promoted that way all along. So once everyone finds out he's evil as hell now, they'll flip their $hit, because they won't see it coming. At all.
We (the hardcore fans) will see it coming and that's why Ed at first said "Some people won't see it coming." Some referring to average players who think Liu represents good.