Well. That's what I love about Galactica, is that it constantly surprises me.
Okay, some thoughts and theories...
Starbuck: Either she's a previously unknown 13th Cylon... or she was resurrected by this remake's version of the Crystal Barge?
Duella: ...well, damn.
Earth: Personally I think that the Colonies were an offshoot of Earth, and not vice versa, as everyone on the show has been led to believe. But Rich has an absolutely frakkin' great theory...
This show has not been a remake at all, but has in fact been a continuation of Galactica 1980.
Think about it: the original BSG takes place somewhere around the 1960s, as Apollo catches a transmission of the Apollo 11 moon landing. Then the Galactica finds Earth in 1980. A human-looking Cylon finds the Earth in "The Night the Cylons Landed." Those are the established facts, of what actually aired.
So suppose the original Galactica fleet ends up in a climactic battle with the Cylons following them, but the new human-looking Cylons end up defecting and joining humanity. (I can just picture it, a wondrously cheesy 1980's scene with the human Cylon saying "What are these things called emotions that I now feel?!? We must help the humans, not destroy them!") Together, the Colonists, the Old Human-looking Cylons and Earth defeat the regular Cylons. The Colonists and Old-Human Looking Cylons settle on Earth, now confident that the Cylon threat has ended. They begin interbreeding with humans (stay with me, here) for centuries, to the point where human and Cylon DNA are now completely intertwined and "pure" humans have died out.
But wait! It turns out that there were still "original" Cylons left in the universe, and the remaining ones have finally found Earth. They nuke it, but are also destroyed themselves in the battle. The "Final Five," who are just regular members of the new Cylon/Human race of Earth, have already been trying to set up a template to recover the lost art of downloading themselves, and have just achieved it at the time of the battle.
The survivors of this final, apocalyptic showdown head out to the stars... find a new planet to settle, that they name Kobol... from there, they settle twelve new Colonies... and over the course of two thousand years, their history is forgotten, confused and jumbled. Earth becomes a legend. Mankind creates their new Cylons. The Cylons rebel. After the war, they shut themselves away from humanity... And They Have A Plan. It's the plan that the Final Five set in motion-- the New Cylons discover their works, create their own human Cylons using their template, and the "Final Five" become the first five of the new human looking Cylons. But from there they can only create 7 new templates, which is why there are only 12 models. They think this plan left behind from the Original Human/Cylons is their call from God. Enter the new series...
Just a thought. ;)