I liked how Minister Jaro (Langella) and Vedek Winn were clearly allies, and you think "Oh shit, those two working together will be a real problem" but then their alliance unraveled over certain philosophical differences. Both seemed to truly have the best interests of Bajor in mind, which is how they'd gotten as far together as they had. But Winn was willing to cross some lines that Jaro wasn't, and vice versa, and things came apart for them.
The best villains are the ones who are intelligent and believe that what they're doing is right. If you're lucky, their means are ultimately their undoing, as former allies go "hey, wait... I never said we'd go that far". If you're not lucky, well, the bad guys win.