Haven't leveled an Agent yet, but I loved watching my friend's playthrough as we leveled together. Looking forward to doing my own sometime soon, since he made choices I wouldn't.
For myself... I love my Bounty Hunter, but for a single favorite chapter, I think I may have to pick Sith Warrior's chapter 1. I had so many
(relatively speaking) choices of how to handle interesting situations, and even if the effects were only short-term, I enjoyed the feeling that I was making policy decisions on my own terms, and not just making simple "kill or not" decisions like on my BH.