At the end of the second season, I was personally disappointed in the episode "Downloaded", because it represented a moment of transition for the Cylons without the necessary context. Caprica Six and Boomer decided to change the Cylon philosophy towards Humanity, and this was depicted as a deviation from The Plan. Unfortunately, The Plan was shrouded in mystery, so it was hard to recognize the extent and depth of what was coming.
This episode has a similar shift, but the writers took the time in previous episodes to set the stage for the schism. Everything since New Caprica has been prologue to the revelation of the "Final Five" and the effect on the Cylon as a whole. The boxing of the Threes permits stalemate. The current Six revolution (led by "Natalie") is most interesting because it facilitates the transformation of Cylon culture.
It suggests, very strongly, that the Raiders and Centurions were operating under complete programming restraint to follow the will of the seven known humaniform models. After all, previously, those seven models were essentially in lockstep. Now, the emergence of the Final Five could have triggered the Raiders towards free will, and now the Centurions have been given the same. They want to understand their origins as well.
This again plays into the idea of a possible ancient origin to the Cylon within certain Human genetic bloodlines, supporting the "cyclic mergence" theory. It's known that the humaniform Cylons can breed, so odds are good that the children can breed. The Cylons of the First Cylon War were all robotic. Why, then, would they designate twelve models above and apart from the robotic and cyborg types? Why would seven of them be aware of each other, but the other five not be? Is it possible that the Cylons only created seven models, but were programmed to know that five others existed somewhere else?
That said, Cavil's decision to break the deadlock with Boomer shouldn't have led so directly to the decision by Natalie to start a revolution. She never presented a firm challenge to Boomer's right to a vote. After all, if Cavil began with the precedence of it, Natalie could have easily demanded that all versions of every model should be given an equal voice. Or she could have demanded that Boomer's right to vote independently be justified or debated. Whatever the case, it seemed more like a plot convenience than a logical progression.
Back on Galactica, the story is less active. Lee officially departs to his new job as a member of the Quorum of Twelve. This positions him rather well to be Roslin's potential successor, since her health continues to decline. Given his early association with her, this would be fitting. In contrast to the obvious conclusion that Kara Thrace is a Cylon, this change in Lee's status makes him the perfect candidate. If nothing else, it would certainly make his comment about Zak in the premiere a case of clever foreshadowing. It would also put him in the perfect position to facilitate a Human/Cylon accord.
All that said, his departure felt interminable. No less than three scenes covered the necessary emotional requirements. Everything was taken care of in the final scene, rendering the scenes in the rec room and the ready room a bit moot. It felt like the writers needed something to fill the time, and they pushed for sentimentality. (The time might have been better spent on Racetrack and her game of Strip Triad; Leah Cairns in civvies would be more than worth it!)
Despite the rift that it threatens to create between Adama and Roslin, there was little question that Adama would ultimately throw his support behind Kara's claims regarding Earth. Not full support, of course, because that would be incredibly foolish, but enough to get the job done. I suspect that this will eventually put her in contact with Cylons of similar vision, though that is obviously nothing but speculation.
The final item of significance is Baltar's new relationship with Tory. It begins as subterfuge, but I suspect it will turn into a significant plot point. The writers again went with over-convenience by giving Baltar just the right metaphor to use with Tory, but the presence of Head!Baltar made up for some of the disappointment. Is that Head!Six messing with Baltar's mind, or has his own subconscious manifested in a new and disturbing form?
The end result is an episode that is a bit slower than the premiere, and given that it was essentially the resolution of a cliffhanger, it felt like something was missing. The potential for a true Cylon civil war has potential, but the events on Galactica could have been equally explosive. Instead, they were more of an emotional counterpoint, and that may not have been enough.