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My BSG Theory
The rumours of this final season is that there's a radical twist at or near the end of the series. A thought just occurred to me... what if the 'skin jobs' aren't actually cylons? (warning: complete speculation based on what we've seen so far follows)
We've heard much about the 13th tribe in BSG, a tribe that went to seek earth while the other 12 tribes colonized other worlds. We've yet to be introduced to that tribe, however, with the exception of the relics and ruins they've left behind. There has conceivably been a couple thousand years of technological evolution since that time. It's entirely possible that while the 12 colonies developed external mechanical artificial intelligences to act as colonial servants (and we know how that turned out), that the 13th tribe turned their technological development inwards.
There may be only 12 copies of the non-mechanical cylons, but there are many permutations of identity within each of those models. They share common traits, but how those traits are used to shape personality can vary wildly, as we see happening with the differences between Boomer Sharon and Athena Sharon, for example. If the 13th tribe tribe developed the means to separate the consciousness from the body and provide effective immortality, then the body itself starts to diminish in importance - the body becomes about as important as the type of car you drive. Why not just have 12 different models to choose from?
After thousands of years, perhaps the 13th colony decides to send out emissaries to the 12 colonies. On the way to finding them, however, they run into the cylons, who are in an active war with the colonies (this would be pre-armistice). For whatever reason, perhaps due to their reliance on technology for their own individual existence, the 13th colony sides with the Cylons. They lend the cylons their own technology, which is a fusing of the mechanical with the organic (and this perhaps gives the cylons an advantage by allowing for faster/more efficient processing of data). The initial outcome of this collaboration is the hybrid we see in BSG: Razor, a first cut at combining organic and mechanic.
The 13th tribe emissaries aren't willing to become part of the cylon empire, however, and there's an internal power struggle. This requires the cylon's attention, and they break off the conflict with the colonies to deal with their own internal power struggles (which the 13th colony wins). Obviously, the 13th colony comes out on top, the cylon race is lobotomized (though one group of centurians and a hybrid manage to escape), and a new series of subservient organic cylons is created.
Perhaps four or five of the original emissaries are opposed to building a new cylon empire and defect to the colonies to live in secret. The other seven remove all references to them from the collective consciousness to prevent future unrest within cylon society, and program future generations of cylons to have an aversion to thinking of their very existence. Cylon society is predicated on agreement among the skin jobs; if there is a significant schism between them, they can't move forward in their plans. Even the memory of the schism would be enough to set them back.
The seven that remain build the technology for resurrection (or replicate it based on their homeworld), and start building the foundation for the eventual attack against the colonies. Keep in mind the resurrection ships are, from what we have seen, exclusively for the skin jobs' use.
One of the things that makes me think this might be the back story is the fairly radical change in design of the raiders, the base stars, and the cylons themselves. The cylons we see after the attack on the colonies are radically different from those we see before the armistice. Something that the audience hasn't been informed of has to have happened to cylon society to make that radical a change.
The final clue for me is the discussion of religion throughout the show. The colonies have a multitheistic religion that roughly matches the separation of the colonies - the Lords of Kobol. The cylons are monotheistic, worshiping a single god. It's interesting to note, however, that the monotheism of the cylons doesn't rule out the existence of the Lords of Kobol, but rather positions their god above them. Likewise, the colonists' religion includes the cylons' god, but positions him/her as being cast out of the Lords of Kobol.
Try and think back to when the thirteen tribes originally separated at Kobol. Why did the 13th tribe go on their own, in the opposite direction from the remaining tribes? It could very well be due to religious difference - enough of a religious difference to create a schism that drove them to leave the collective tribes, and a religious difference that would grow deep into social consciousness over a couple thousand years, and could be used to indoctrinate a nascent society (the cylons) into their way of thinking.
So that's my theory, that the skin jobs are in fact the 13th tribe, and that they assimilated the cylons for their own ends. I guess we'll find out in the last half of the season.