I think the trouble (or intriguing thing, depending on one's pov) people have with both of them is that they don't fit easily into archetypes people are familiar with. Six is neither the cackling villainess nor the "good bad" girl (Sharon in the first season came close to that one, though she left that behind later, starting with "Home" in sII, I'd say), i.e. the Bond girl who first does the villain's bidding and then switches sides because she's had sex with the hero. Baltar isn't a cackling villain nor is he a good bad boy, i.e. someone cool and hip who just fights on the wrong side. They really don't have precedents, and so we're challenged to constantly reevaluate them.