I dunno, the big viewer issues with this episode seem clustered around the characterization of Galen and Ellen, and I don't really see a disconnect there. I didn't feel Ellen was hugely sympathetic in the last episode, because as much as I like her, and liked her, she was pretty manipulative then too. It's a certain sort of passive control Final Ellen exerts over situations that isn't even really at odds with the Ellen we met so long ago. She did that shit with Saul when Bill got shot, all "I believe in you so much, don't blame yourself, take control of the ship."
Maybe it's confusing because we're not used to seeing that sort of unctuous nurturing passive-aggression on TV -- well, Laura Roslin is a master at it -- but I thought she and Cavil were pretty much evenly matched, in their divergent arrogance and the way they used Boomer's busted ass for their football: "See what he did to you?" "See what she did to us?" "I love you like I love all my children" isn't all that different from "I'm teaching you to be a better machine." And frankly, "I love you because I made you" is about the grossest thing you can say to a person, because it turns family from a bond built on love to a pair of creator-god handcuffs that I can't abide. So seeing her pull the same shit on Caprica, or being driven by her lesser angels in the whole "stay or go" deal, not that surprising.
Same with Galen: if you bought the whole "be my Chief" thing as some sort of Come-To-Jesus where everything goes back to status quo, then his actions in this episode make no sense. But I mean, his wife died and he spent weeks in a downward spiral very busily and deliberately setting fire to his entire life, we watched that happen, and the only thing that kept him tethered to his humanity was Nicky, who was of course taken away from him in a pretty fucked-up way. My understanding is that he's been living on the Baseship since around that time, so this has just been him coming around to perform as "Chief" on a freelance basis, having been asked to do so by Bill, with whom he's always had an intensely complex relationship anyway. What's left to connect him to Bill, or the Fleet, besides our affection for him?
Leaving the Fleet -- which makes total sense for even the 268s, especially now that Ellen's home and Caprica's knocked up with a magical Cylon baby -- is a betrayal, of a kind. I guess. But I don't see it as much different from Bill's insistence last week that the upgrade team consist of humans, or the fact that Boomer went directly to the brig. And I know it's fun to hate Tory, for saying the true shit nobody else will say. So I guess it's hard to imagine him agreeing with Tory, no matter what the question is. Saul said he would be the man he's chosen to be, until the end; Sam Anders sees no horrible distinction between his selves; seems now to find the entire prospect beautiful. As I would hope anybody would, given enough time to adjust.