The really shocking thing is that the Cylons were not created by man which is what the original premise of the show was.
I think the truth will end up in-between: the Cylons WERE created by Man, but secretly influenced/helped/controlled by the ancient Cylons. (Which is why I wonder about the new Caprica series.) Of course, those ancient Cylons didn't use the term Cylon--that's a recent word. Maybe they just thought of themselves as a type of human!
We already knew that Saul was around at the time of the FIRST (Centurion) war. So the Cylons were up to more than anyone (even the known 7) were aware, even back when the human-made Cylons were "young."
Is there some sort of time travel aspect to the story now. She disappeared in season 3 then returned after going to Earth? Is the dead Starbuck the one that we saw from seasons 1-3 and the current one a time travelling one? Great show. I will be sorely disappointed when it ends...
I'd say Starbuck is a Cylon, except that makes one too many Cylons! Then I thought she might be an Ellen model, and will look like Ellen when she ages... except Saul would have seen plenty of young pictures of Ellen. Doesn't really work. I guess she could be some whole other Cylon category, like the Hybrids and the Centurions.
We also don't really KNOW who that corpse is, we only know whose dogtags it was wearing. So I say anything's possible--but time travel doesn't seem likely to me. That would seem to stretch the bounds of the series. A faster-than-light jump from the maelstrom to Earth as she exploded would be within bounds: FTL technology exists. But then exactly who transported her (in both directions)? I would have thought Leoben in a Heavy Raider... but he seems completely surprised by the whole thing. I think strings are being pulled by parties (the ancient Cylons?) that we haven't seen yet.
SERIES-END SPOILER WARNING (just my own theory, though):
I also think it will turn out that the the 13th tribe didn't go TO Earth... they went BACK to Earth. And that humanity (and/or Cylons--the two races must have some relation) came from Earth to Kobol to begin with. Meaning, we today are living the beginning of the whole story. But are we the race known on the show as humans, or the race known as Cylons?
I think we're humans, and that we'll depart (some of us? all of us?) for Kobol someday, and then when the 13th tribe (the Cylons) flees to Earth (finding it empty? defeating us remaining humans?) that will be the start of the Cylons on Earth. Which makes me think the Cylons were created on Kobol and then fled their "masters" back to Earth, OR that the Cylons were always on Kobol (possibly they were the "gods." We don't really know what catastrophe caused humanity to flee Kobol: maybe the Cylons caused it.
It's also plausible that the Cylons were created here on Earth, and they DROVE humans to flee to Kobol (maybe with some secret Cylons along as well). If that's the case, the 13th tribe doesn't have to be Cylons after all--they could have been humans. The Cylons were ALREADY on Earth when the 13th tribe came back. (Did the 13th tribe of humans then nuke the Cylons on Earth?)
And remember: Six said that the Cylons know more about Colonial religion than the humans themselves. That implies a Cylon-Kobol link.
EDIT: The more I think about it, the more I think that the Heavy Raider (operated by who??) rescued Kara from her Viper's explosion and she never died. Remember, she had her hand on the ejection lever, and Heavy Raiders can carry people. Then, whoever-it-was planted Kara's wreckage on Earth, including putting Kara's gear on some other body. Lastly, they gave Kara a new Viper, primed to seek out the beacon of the damaged Viper. Kara remembers little of this of course. Who did all this and why? I think it has something to do with the "plan" (mentioned by ancient-Ellen) of the ancient Cylons.
I used to think the big Cylon "Plan" was nothing more than religiously-motivated genocide (no secret) plus a Cylon-human breeding program (secret at first). Then Caprica Six and Boomer convinced them to change the Plan (at least the genocide part). But NOW I'm thinking the Cylon Plan may be much larger (and older), and that even the Cylons themselves don't know it yet!