The wild cards in the BG saga are the Centurions. With the inhibitor against higher functions removed, there is nothing to stop them from accumulating information and experiences with both humans and skinjobs, and forming their own conclusions. There is also the wealth of information available to them in the Cylon databases about Cylon history after the first armistice was signed, something that the humans no nothing about.

What conclusions they might draw is impossible to say, but judging from the fact that they require courtesies from skinjobs to do their assigned tasks means that they already consider themselves equals, which is a dangerous precedent as the Cavils pointed out. Who knows what new demands they will make?