As above, in a twist of the origins of the war, some cylons start to turn against their own masters - the cylons themselves. The dissent spreads from Anders, and also via Six (more later). They will, ultimately, make a complete sacrifice and kill themselves and as many other cylons - possibly all. Why? Because they will come to believe that this is what God wants. Religious ferver will push them to that action. They'll believe they've been led astray. They have become too human and have begun to empathise with the humans, heck some think they ARE human, they love them even (Anders-Starbuck, Six-Balthar) and it will be their belief that they have to help the humans. They'll believe this is what God wants. It'll be a last ditch action..they'll try to convince the others, but ultimately their only recourse will be to destroy themselves.
There were hints of this kind of dissent as the humans got to New Caprica..but now, the dissenting Cylons will know that they can't risk letting the Cylons stick around, since they know what happened last time.
This would mean..the humans get to earth, relatively safe and sound. It would resolve the question of the Cylons.
It would resolve some other questions too:
The final five are literally the final five - there will be no more cylon models because the cylons will destroy themselves.
Hera's importance - she is the future of the cylons, because she's the only one who can survive whatever mechanism the dissenting cylons use to destroy themselves and the rest. She represents the cylon's future as a part of surviving humanity. Maybe Cally's baby too, but the Cylons don't know about her. This is why she's so important, she literally will be the only trace of Cylon left (I guess..).
Balthar and Six - Balthar was indeed part of God's plan. Six fell in love with him. Her (conflicted) empathy with humanity has been visible from the start (the baby in the first episode, sparing it...her comments on Caprica, almost sympathetic to the humans). Balthar's role was, to make her fall in love with humanity, effectively. This, I'm figuring, makes her model vulnerable to Ander's 'virus' and made her the best candidate for "evolution", and to lead the dissent on the ground, amongst the cylons, with the help of D'anna who was perhaps getting close to 'God's truth' herself before Cavel boxed her (hence her "i'm so sorry" moment to one of the final five?).
There are many other threads to tie up and I'm not sure if they'd all fit in..but that's my best guess now. They get to earth, the cylons disappear through dissent and self destruction, but of course, it's bittersweet because Tigh, Tyrrel, Anders etc. are dead. Along with whoever the final Cylon is (presumably someone very key, who'll make the whole thing even more bittersweet).
