"God"/deus ex machina nature of the ending. The argument goes that if God is all-powerful, his "plan" at the end is sadistic and nonsensical.
I agree that if you assume the Cylon god is an all-powerful monotheistic diety, the whole story and the ending/epilogue make zero sense. However, what I took from the show is that the Cylon god is just another pagan god, like the Lords of Kobol. However, this pagan god thinks he is awesomer than the other gods and should be worshipped over all others. Just because the Cylons say their god is the only god, does not make it true. In fact, the Cylon god could be one of the Lords of Kobol themselves (wasn't there a religious war on Kobol before the Thirteen Tribes fled to the colonies? The idea that the Cylon god is a fallen Lord of Kobol is also supported by the repetition of the opera house vision, which I believe was on Kobol.) In other words, the Cylon god is NOT all-powerful, he just wants to seem that way. And he has his own agenda for the future.
This would also explain the whole Starbuck thing, which seems to me like a reference to the original series. Wasn't that Starbuck also "tested" and resurrected as an angel? Kara Thrace was tested by head Leobin (an angel), passed the test when she embraced her mother, and was resurrected as a new angel in the pagan god's service. She just didn't know about it until she got to our Earth, after which point she was able to disappear at will. Head Gaius and head six are also servants of this pagan Cylon god, who is probably just some super advanced alien being. They know what they are and are therefore able to utilize their powers to appear to only those people they want to appear to.
The "plan" is to create a new civilization that does not serve the Lords of Kobol, but that only serve this one Cylon god. The Cylon god obviously is full of himself and thinks that he and his teachings alone can stop the cycle of violence between man and machine, and most of the events of the BSG series were orchestrated to get mankind and the Cylons to earth while shedding the old gods' ideas (the eye of jupiter, arrow of appollo, etc. show that the Thirteenth Tribe, on the other hand, did not abandon the Lords of Kobol. According to the Cylon god, this is probably a contributing factor to the cycle of violence.)
). I haven't watched Caprica. I also have no idea how to explain the ridiculous decision to
