Storywise Mileena would be easy to put in.

I'm more worried about the variation-thing with Mileena. In over 20 years, the MK team didn't really knew what moves to give mileena other than her teleport, sai throw and roll, after years she finally gained the biting-thing... but seeing how lazy they are over Mileena's moves, I can't see them create three variations for her. Sure we know she could use Sai's more in one variation, but that leaves two variations. For the same reason I fear for Tanya, but at least that would be easier than Mileena, which left them inspireless for over 20 years.

And now with this Kotal Kahn being the emperor of Outworld so suddenly, that is probably easy/lazy possibility to skip Mileena and a hard time thinking about giving her some new moves finally after 20 years.

I really hope i'm wrong.

Is it possible they meant he is an actual Mayan deity?

No, because that does not fit with Mayan lore.

Stupid objection. This is a video game.