The basic plot premise doesn't quite make sense. Pythia recounts the visit of the 13th tribe to Earth, but how would we know about that unless there was a return journey? We're also led to believe that the Lords of Kobol were real, but that's not really followed up on.
Easy fix: Make humans the real 'Cylons,' who were created on Kobol but rose up against the humans, only to colonize elsewhere and leave behind resurrection. The real humans return home to Earth, and their story is conveyed back by continued visits between Kobol-Earth-Colonies. You can even toss in a few more cycles in here to leave everyone confused about which came first. I thought this is how they were going to go when I first saw the series.
Kara and Baltar are both half-Cylons; their father was Daniel, the number 7. They see 'angels' because they have the capacity for projection, but these are essentially inner drives. Kara's resurrection now becomes reasonable enough to imagine--and presents hope for humanity.
The Cylons do have a "Plan"; remember how the keep finding the Colonials, only to give them just enough space to get away? They want to keep them alive, because they're looking for Earth as well.
Going down the dark road and killing off virtually everbody would be nice, but it's a little too easy. But you can have them find Earth--our Earth, in the future--have the Cylons show up too, as they've been following, and you can destroy Earth. All the religious folk are completely discredited.
Not sure where to go from here, but resorting to deus ex machina in such a literal fashion is a little disappointing.