While I agree that I don't have a clue whats going on, I'm starting to think that neither do the producers.
Like I've said in another thread, the shows quality has dropped since season 1, and most dramatically in season 3. The religious aspect of the show, while initially class and seemingly very deep, just seems, to me and two friends at least, contrived in the most recent episodes. The whole 'Eye of Jupiter' just seemed like something that was thought up just for that small plot loop, and while I know that both the Cylons and Humans are supposed to be winging it, it just doesn't make for convincing universe history. Saying that though, they have been some of the best episodes of this season. It's the fillers that are really bringing the show down. The most recent ep; in which Helo tries to manage the infected refugees and sagitarons was pretty bad. Very misable. The Apollo/Duawla(?), Starbuck/Anders was the only mildly interesting part and even that felt contrived.
It really annoys me considering it used to be really great and worry about it getting to its finish, even though its already gotten at least half a 4th season.