Come now, the Season 3 episodes dealing with the occupation weren't bad, especially Exodus 2 and the Pegasus getting destroyed. Also, I liked the 'court drama' trial of baltar/reveal of final 4/crossroads episodes.
What was filler was the Baltar on Basestar crap.
I personally think it's Gaeta = Final Cylon. Remember when Shelley Godfrey turned up with that photo showing Baltar betraying the colonials, and Gaeta goes from showing baltar guilty to proving his innocence in a snap?
Adama/Roslin/Starbuck/Gaius are too obvious. Besides, comments from Ron Moore pretty much eliminate Adama/Roslin/Gaius (he said no one in the Last Supper picture is the final cylon, e.g.
The show has previously hinted the final four. For example, when Chief Tyrol was on the Algae planet, he got a sixth sense of the Temple of Five, and before that, he went insane, beat up Cally, and sought religious council with the Cavil cylon model because he thought he was a cylon, just like Boomer got suspicious.