Here's my take on Season 1 and what I think is the main story behind all the mysticism.
I think that everything has been perfectly orchestrated by the cylons. We have seen how Starbuck can go in a Cylon Raider to Caprica from the vicinity of Kobol in a SINGLE JUMP.
We know that most of the time, the Cylons know where Galactica is (they do have spies on the fleet), and we have seen raiders jumping in, watching, jumping out.
And we have watched how the cylons desperately need "love" and feeling human. It's as if they needed human contact in order to fulfill their existence.
I believe that the cylons are using the prophecies in order to guide the fleet to the place they want and make things happen in such a way that they make their way into them, blending with humans and being accepted.
As a matter of fact, the fleet has been somehow "coaxed" into going to certain places: Boomer blowing up the water reserves, Baltar being "guided" by Number 6 and her "god"...
That brings me to the conclussion that the president, with her very lucid visions and faith in the prophecies, has to be a cylon.
Adama... well, he is reacting like a soldier, so it's not necessary for him to be a cylon to make the decissions he made... then again, Sharon ***************** at the end of the last episode made me think twice... why would she do that? Was she influenced by her cylon persona or by her belief that she's human?
But there are some loose ends: the prophecy says that everything happens again, "a la matrix". Is this an iteration of an experiment of the cylons?
God this series is good.
Daniel