Scorpius gets so interesting that a time will come where you may
not even want to call him a "villain" at all.
Farscape is tricky like that. It's not black-and-white, good guys vs. bad guys all the time. Remember, the "good guys" are escaped criminals,
and the "bad guys" are people with their own goals and motivations. They aren't just evil for the sake of being evil, even if they do dress in scary black leather.