Ron Moore has recently conducted an interview with Pegasus Galaxy, where he's provided some interesting answers for questions: There are some possible spoilers for elements of season 3.
PG: And where is Zarek now? We missed him in the last half hour of the finale.
RM: He's the vice president of the colonies and we'll pick him up next season. There were just so many players to have to deal with in the end that we couldn't get to him. He's down there and he's actually a bit disillusioned with Baltar and the whole administration and what became of this whole project.
PG: We wondered about that…how things got so bad in just one year. And where Sharon went, too...
RM: That's all stuff for next season.
PG: Are we ever going to learn why Baltar has Six in his head and vice versa?
RM: Yeah, we'll get more into that. It's one of those things I want to tease out over the course of the series.
PG: Are you going to explore more about how the Cylon culture developed – about how, if they were machines, they evolved into this more human culture?
RM: Yes, we'll slowly talk more and more about their evolutionary process and where they are. One of the things we want to grapple with in Season 3 is that they are a very young civilization, a very young society – a lot of the rules and ideas that they have had are very formative ones. They have just come up with a lot of these notions and they are exploring them. Like in Downloaded, it was a culture based on homogeneity, and now they have people who are starting to break out and have differences and certain divisions are setting in, and then you saw in the finale that there are even Cylons who don't believe that there's a God, which is a fundamental tenet for the rest of them, so they are sort of starting to work those ideas out and approach those ideas for the first time.
PG: There is a lot of speculation that Baltar is a Cylon because of that. Or it could be more a reflection that she is as hooked on him as he is on her and that the Cylons can really love.
RM: Yeah, that's closer to the idea.
Read the full interview here.