In my head God in the world of Battlestar Galactica was a Cylon created by a civilization predating even Kobol who had evolved beyond corporeal form.
Cavil says "I don’t want to be human. I want to see gamma rays, I want to hear X-rays, and I want to smell dark matter. Do you see the absurdity of what I am? I can’t even express these things properly, because I have to — I have to conceptualize complex ideas in this stupid, limiting spoken language, but I know I want to reach out with something other than these prehensile paws, and feel the solar wind of a supernova flowing over me. I’m a machine, and I can know much more, I could experience so much more, but I’m trapped in this absurd body."
God was a Cylon that achieved Cavil's dream.
This Cylon (God) seeks to end the cycle it has seen occur over and over again and takes steps throughout the series to make sure this is the end.