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My crazy theory
Everyone has a pet one of these, so here's mine. So, so many holes in it:
1) Humans on planet A live alongside a race of "gods" who walk among them.
2) For some reason the "gods" leave planet A and head into the stars.
3) Thousands of years pass. The previous stories pass into legend and myth. Humans create the Cylons, who eventually rebel, develop human form and all but annihilate the human civilisation. A remnant of humanity is forced to flee to the heavens. Around this time the "gods" rejoin them.
4) They are pursued by the Cylons who quickly tire of the human planet and search for a new home.
5) Growing weary of fighting the humans and Cylons eventually settle on planet B, together. They interbreed and come to regard themselves as a singular "humanity" once more. The "gods" (who found B in step 2) take their previous place once more, and everything is at peace. A few thousand years later...
6) Go to step 1.
All this has happened before see! Effectively humanity and the Cylon perpetually hop around the galaxy shooting at each other, diverging and merging.
I'll now drift even further into the realms of implausibility in the cause of elaboration:
Separate from the cycle are a small band of Cylons. These are the "gods" mentioned above. Maybe one is added to their number each cycle? Nevertheless, there are currently five of them, and they have a pretty cool clubhouse, which was built after they Kobol in step 2 (where they had an even cooler clubhouse) Did I mention the 13th tribe were Cylons :)? They're job is to keep the cycle going. (Perhaps in the beginning Earth's humanity realised only this bizarre cyclical pattern could keep the species alive?) So they prepare the roadsigns and all that, help the new cylons to develop human form and shape bits of the religions to their end.
Eventually a handful of their number enter the population and are deliberately made unaware of their nature until a wake-up-call at the right time.
What we are seeing now is only the latest iteration in a cycle which has been repeating for millennia. When the fleet do reach Earth, they find the charred remains of previous earth civilisations, including ours. (I want to see Adama kneeling down before a toppled Statue of Liberty: "You Frakkers! You blew it up! Ah, frak you! Gods frak you all to hell!")
Oh yeah, God (RDM) or something like him oversees the whole shebang. Starbuck, Baltar, Roslin and possibly others are fulfilling specific roles under God's watchful eye that have been played out by others in the past.
I have a few ideas how this explains a few things in the show, but they'll have to wait.