Here's going out on a limb.
I thing we'll find when they get to Earth, the fleet will discover the origin of the 12 colonies WAS earth. Think about it. In order for the old scriptures from the 12 colonies to be able to predict or describe in some fashion what the path to earth might look like (the eye of Jupiter and such), they would have had to go that way first, get to earth, and then come back. Otherwise, how did the 12 colonies and the Lords of Kobol know to write about the journey and its markers in the first place? You can't draw a map to a place you or anyone else has never been. "Life here began out there". The colonies originated on Earth, went out to start a new civilization and left a trail of "bread crumbs" along the way (like the beacon with the encephalitis infection) to let future generations know how to get back. That might also explain why their references to the greek gods and our signs of the zodiac are so closely related (and they all speak english). Now the speculation begins ... Why leave earth in the first place?
Maybe we destroyed it to the point that it couldn't sustain life anymore and they had to leave. And now with thousands of years gone by, it might be all nice and green again. Except nobody lives there anymore.
Maybe there were earth-originated "cylons" who created the humans who then rebelled against their creators and one of the two groups left earth to keep the peace. "All this has happened before and will happen again".
Maybe an older version of cylons that began on Earth decided to worship the greek gods and a religious war forced them out into the "heavens" and then they founded Kobol. Being of superior "construction" they could call themselves gods and rule over the humans they brought along with them to Kobol until their dictatorship was overthrown. Leoben talking to Kara refers to "maybe last time you were the cylon and I was the human" (or something like that - I'm sure I'm not quoting it right - but you get the jist).
Who knows. There's lots of possibilities. All I know is ... I'm going to enjoy going along for the ride with season 4 to find out what happens at the end. I haven't been this interested in a singular television show since Millenium (remember that one?).
Kudos to Ron Moore. You're doing a great job.