As for wanting to be organic / human, remember that what the Cylons want freedom from is oppression and being used as disposable people. The First Cylon herself wanted to be human again and didn't see the joy in remaining an iron plated robot. It hasn't been revealed just what connection she has, if any, to the rebellion. Could it be that the Cylons, before the arrival of the Five and the manipulation of Cavil, wished to find some form of hybrid form that allowed them to feel some form of humanity while preserving their mechanical advantages?
Based on "the shape of things to come" montage at the end of Caprica
, Zoe-A eventually gets a hybrid organic/synthetic body that her parents create for her. However, I feel like she's a special case and not a representative of the cylons as a whole. In fact, I'd go so far as to say that Zoe-A has nothing to do with the cylon rebellion. Otherwise, we'd see other cylons during the war with the same hybrid-type of body.
The cylons featured in B&C seem to be the next stage in mechanical evolution, bridging the gap to the new, sleeker models seen in nuBSG. The cylons were clearly interested in evolving into organic bodies, hence the experimentation and the genetic engineering (like the giant snake/eel thing). They weren't terribly successful, though, until the Final Five arrived and helped them develop the 12 human models. But even after that, the cylons still have synthetic/organic hybrid technology in the base stars and raiders, and they even still retain fully mechanical centurions as their foot soldiers.