As I understand it, the villains have already been added in as night creatures, entity position holders, bandit leaders, and necromancers. What this update will do is give them goals, and have people move around and potentially do bad stuff so that killing them actually serves some sort of purpose. Also, it says on the dev page that villains are just leaders of groups you oppose, so we should expect some moral ambiguity.
Also, personal prediction, I expect all the NPCs to be (more so than intended) sociopathic about pursuing their goals. I say that based on a story about the early development of Oblivion: they originally planned to have NPCs go and do stuff on their own with a goal based system much like the one DF is supposed to have. For one of the tests, they gave one guy a rake and one a broom, and told the rake one to sweep the floor and the broom one to rake leaves. The guy with the rake decided he needed the broom, so he killed the guy with the broom, then took his broom and started sweeping the floor like nothing happened. And this is DF, so you can expect the glitches to be a bit more... extreme. Like, hungry elves will consistently attempt to kill the closest humanoid and butcher them. Whatever it is, should be fun.