While skimming through a bit of season 2.0 I stopped at the scenes where Six and Boomer wake up in the pod-of-goo. I was struck by two things. The first was how much connection both of them upon waking up had with their former lives. They seemed to be very concerned with what (to them anyway) had just happened.
The other thing that caught my eye was how concerned that the “brothers” and “sisters” seemed to be about her well being, almost as if they were worried that their sibling had been infected in some way.
I wonder if in their quest to carry out whatever plan that they are doing, if the human emotions and values they run across might have an adverse effect on the cylons upon waking up in a tub of goo surrounded by the very things that previously the group you were with, were deathly afraid of. Boomer screamed in horror upon realizing that she was, in fact, a cylon and that not only was she not unique but that she could never go back to her human friends and family.
The cylons are obviously great creators, but in their creation of human looking and acting beings they may have made a costly mistake. They are like us. They can feel emotion, they can think for themselves. I wonder how long it will be before the humans start fracking around in the heads of cylons just as they have but doing to them. The sword swings both directions. If you can think, you can second guess as well.