So....the revelations of "The Farm" lead me back to some of the fundamental questions of the story.
What is the Cylon's purpose in trying to re-create humans as closely as possible? They have the 12 "clones" and there are many copies of them. But now we find out they are actively trying to make new baby Cylon/humans.
Why? There is no significant human population left to infiltrate and defeat. And if there is, the machine Cylons can readily destroy them. Unless...the Cylons have exhausted the resources of the 12 worlds and cannot make any more machine Cylons? (I am admittedly in blatant speculation mode here.)
I understand that their religion tells them to destroy the humans, but at the same time tells them that the events of the story are all part of a great cycle that has happened before and will happen again. It's chicken-and-egg, isn't it? They are just fulfilling their destiny?
Doesn't that make them direct idealogical descendents of HAL 9000?!?! He did evil, but he was not evil. It was
us that was evil and programmed him as such by our nature.
So I go back to the idea that was floated here in the last few days, they are trying to reproduce because they have a societal survival instinct? And they wear out, just like any other machine? That's not hard to swallow. But do they need to hunt the surviving fleet to do it?
There have been so many good stories about robots outwitting humans and outlasting them in popular film the last 35 years, (going back to 2001:ASE) I think Ron Moore is using that against us as we try to figure out where he is going with this!

Of course, this could just be one big religious allegory that ends with no answers as to the definite motivation of the Cyclons.