I was going to say Daenarys until I saw you covered her. But these things start small, man. Some reasons why it could happen:
a) She'd be the most well-developed villain in TV history, and would make the end-game fascinating;
b) There's been plenty of foreshadowing if it goes that way; her family is evil and she has done some vicious things and suffered terribly; and
c) It would really fucking upset a lot of people - which GRRM and the show's runners seem to love to do.
Probably more likely that Jon and Dany ally in the end, but Dany going closer to mad queen or evil queen status after the total collapse of Mereen would be far more interesting.
I've been avoiding this thread due to fatigue over the 'scandal' so I may have missed a lot, but I don't think Dany's family was evil? Just her dad
Ser Barristan called Rhaegar the greatest man he ever met. I mean, he did 'kidnap' lyanna, but that is probably because he knocked her up. Viserys wasn't evil, just arrogant and obsessed. He was no more evil than, say, Tywin
The Bolton's days are numbered. Whether Stannis defeats them in battle, Sansa and Theon kill them, LF kills them, they aren't going to last. Only problem is, who will the major villains be when they meet their inevitable demise? There aren't many main villain characters left at this point, Tommen is nothing like Joffrey, Tywin is gone and Cersei seems to be making a colossal mess that will come back to bite her in the end, even the wildlings are potentially teaming up and they were significant villains before. Daenerys seems to be going a bit mad but I can't see her becoming a major villain.
There are only 2 seasons left, the White Walkers have to show up soon. Little Finger is also a villain in the end, I'd imagine. Certainly he stands in the way of Daenerys' destiny
The rapists on the wall will probably be a brief villain too (again) since they foreshadowed that when Stannis left.
Also the sons of the harpies, stonemen, slavers, melisandre etc.
tldr: I don't think we need to worry about a shortage of villains