It could be almost anyone, but we have evidence we can piece together to lead us in several directions:
- We've been told it's a 'surprising return character' who hasn't been a boss before;
- We know that both Shinnok and Liu Kang are playable;
- We can probably assume that neither Shinnok nor Liu Kang are unlockable, because they have been revealed and played;
- We can safely assume that Liu Kang will be a sub-boss at some point, probably in Revenant form;
- We can definitely assume that Shinnok will be a sub-boss at some point, and is leading the Revenant faction;
- We know there is at least one unlockable character (story mode #1), and possibly more (story mode #2, living towers);
- We can - at this point - assume that the comics are pointing towards Reiko, and that he is probably being set up by Havik.
However, the Reiko/Havik storyline may either change drastically before the game is launched or be a complete red herring to distract us from the real boss.
That said, if we take the above facts and assumptions into account - and I admit some of these may be subjective - then we can probably rule out Liu Kang and Shinnok as final bosses -- at least in human form. Indeed, Shinnok has been a boss before, so technically we should rule him out altogether.
NRS have said that they want to leave us with some surprises, and I don't believe they would reveal (albeit unknowingly, to us) the final boss character and do a variation breakdown for him/her. It looks like Liu Kang starts off as a Revenant (alongside several other dead characters) and must be freed (thereby having his mortality restored) by Quan Chi and/or Shinnok being defeated by Raiden, which is possibly the plot of the first segment of story mode. That would explain how Liu Kang is able to age, and he probably acts as one of Raiden's allies for later parts of the story. (The same goes for Kung Lao, Jax, and whoever else has Revenant forms).
Shinnok is likely beaten early on and then comes back later as a catalyst for the actual boss; he probably fights in one costume and one variation to begin with, and then switches both of these in the later fight, as well obviously being much more difficult to defeat. That'd be my hunch, anyway.
We can probably assume that the end boss is someone who has been possessed in some way by the daggers/blood magic, and is either serving Shinnok or using him for greater ends. Who comes to mind there? Aye, Havik. That's just my guess, though (and a lot of other people's, but you know what I mean) and it really could be anyone, as in theory anyone could be possessed, go 'evil', form their own faction and try to beat everyone else. NRS may well decide to pull the rug from under us by having it be someone like Kenshi or Sonya, but I think that would be purely for the shock factor rather than to make an interesting/believable villain and a coherent storyline.
Unless he is obviously and definitively killed off in the comic then my money's on Havik, but I know that's a really 'obvious' guess based on the introduction he's been given in them, but it's logical, it works, it'd be interesting, and his fatalities and variations could be amazing. If it's not him then I am genuinely out of ideas (and I don't want it to be Reiko, but it won't be).
Fujin would be an interesting choice, and I think it would be a very clever and fun plot device, and it would almost certainly mean he was the unlockable character. I'm all for this.