Androme wrote...
Flemeth as main villain.
Morrigan supporting the protagonist.
While Flemeth may possibly not be the main villain of DA3, I think it's quite clear that Morrigan and Flemeth are by now hostile towards eachother, and Flemeth is up to something big, + in the leaks it says somebody is pulling the strings, Flemeth fits into that description (as I understand it) hence why I suspect the possibility of her being the main villain, but I might very well be wrong.
I'm not sure, Flemeth certainly does have a great deal of mystery invested in many different facets of the lore, however it seems like the majority of the time she is doing it only because her own existence is more important to her than anything else. Examples:
1.) She saved King Maric in the Stolen Throne so that he take back the throne and bring the Wardens back into the limelight in Fereldan, all because she knew that a Blight was coming in the near future.
2.) She saved the Warden so that he could unite Fereldan and defeat the Archdemon, pointedly noting that the Blight would kill her to and that was her reasoning.
3.) She attemps to kill her own daughter as a means to preserve her own life.
4.) She saves Hawke so that he will in turn preserve herself from the Warden's wrath.
The point being here is that I don't feel there is enough information to suggest Flemeth as a main antagonist just yet. It seems far more likely that everything she does is a means to preserve her own life, it just so happens that on the way to that she happens to effect a great many plots.