I called this theory in last night, but I’ve refined it a bit since then. It connects Head 6/Baltar with the “All this has happened before and will happen again” concept.
I’d imagine that most people in the galaxy don’t have major roles to play in the cycle of time. However, not all of those who do have major roles would be willing or able to play their parts without a guiding force. I think the head characters are manifestations of a higher power that wants to make sure that the cycle isn’t broken by providing that guiding force.
Now comes the question of why they’d want the cycle to continue. I think that perhaps they were survivors of the first cycle. Perhaps they were the fusion of the “humans” and “Cylons” from that cycle and eventually ascended to a higher plane while the majority of their races started the cycle again. If so, they may want to prevent anyone else from reaching their level out of fear, so they act to drive the humans and Cylons apart each cycle.