Scorpius obviously has a very passionate agenda, one which he has only minimally revealed to us. So there's a lot more to be divulged in season three about Scorpius' personal journey. And John Crichton, if he manages to survive the operation, must enter season three, obviously, as a different man than he was in season two. Knowing he was the cause of the death of the woman whom he's finally come to realize is the love of his life changes him forever.
Season three will be filled with "what ifs?" for John, what would have happened if Aeryn had survived, what would have happened if he had been able to break Scorpius' control over him.
In season three, Scorpius has a major internal conflict regarding his dual Sebacean/Scarran heritage. He is, as all great villains are, someone whom we love to hate. His motivations are clear, and though we may disagree with them, we at least understand him. He's a great villain.
Next season, the crew will continue to expand and contract. We'll have at least one new character (at least for a while).