I know a lot of people say that Mileena as the big bad doesn't make sense, but that seems baseless to me? I mean, it seems pretty possible. I am kind of hoping it isn't the case because despite it promoting her far from her childish demeanor in MK9, which is what the fans wanted, it would mean that she's unplayable. But I definitely think it's possible.
Kotal seems good enough from the comics, in that he doesn't seem entirely evil and he's not on bad terms with Earthrealm, even if Sonya doesn't trust him. He is also currently fighting a war against Mileena for the throne of Outworld, so she's obviously powerful enough that she can hold her own against him.
So if we know that Mileena's a lot more powerful now, and she's a returning character, wouldn't it make some sort of sense if she came across all the power and was just powerful enough to hold everyone off with her powerful army?
Just a thought; I don't necessarily think they'd make a female antagonist, but I think that it's not out of the realm of possibility.
As for Kotal, he seems to me to be a good version of the two sides fighting for the throne. I think that though he's murderous and all, he's not necessarily evil, and definitely not like Mileena is. Especially since he's willing to work with Earthrealm and save them from Mileena.