I just finished the entire BSG series, watched about five episodes a day from seasons 1-4 over a two week period.
I have a theory about Gaius' final line: "you know he doesn't like that name"...
I think in this final scene we're looking at the "angel" Gaius. And just as Cara Thrace became an angel but never actually met her creator, this Angel Gaius most likely has not met his creator but understands he has one.
When Gaius refers to "He", it is in fact a reference to his all mighty creator, but "God" is a word created by man and therefore is limited. The word "God" would lump his one-true creator with other deities. The entire series plays with the absurdity of worship and honour to those underserving. Take for instance the gods of Greek myth --Zeus, Hera, Apollo, Athena, etc...-- we all know that these gods were closer to being mortal than divine. In one of the episodes, I believe Gaius is the one who points out that Zeus was a serial rapist. The word "god" lumps his creator with the likes of those gods and with Ellen and Saul, with the final five, and yes even with the mortal Gaius who was once worshipped himself as a "god-like" being. I think Gaius would say that man's understanding of "God" is a farce.
Throughout the series, one of Gaius' greatest flaws is his delusion of self grandeur--he lacks humility. So when he blurts out this line "you know He doesn't like that name", he's probably making an assumption and doesn't actually know his creator or his creator's thoughts. When Caprica looks at him, he realizes what he's doing (i.e. once again stepping onto his soapbox) so he immediately retracts his statement, to remain humble.
I think something should also be said about Season 4 ep. 15 when Ellen is resurrected; she is greeeted by model 1 and calls him "John". Model 1 replies by saying "that's not my name, i always hated that name". Model 1 understands that the name limits his character, it makes him a creation in the image of a man (Ellen's father). Model 1 thus rejects the name and any value or meaning it carries.
So to conclude, I think the Angel Gaius' final sentence eludes to the fact that humanity is limited by our linear perspectives. We seek meaning to words we ourselves have created. Words like religion and science, man and machine, good and evil. We divide ourselves with invisible lines in the quest for absolute and final endings. But as long as those questions are left unanswered, as long as we are drawn to scratch that unscratchable itch, we are also destined to repeat ourselves.
