No, the Cylons were human. Completely human. That was the problem. They could even interbreed and provide viable offspring for crying out loud. That's why they were uninteresting.
Anyway, written sci-fi has been doing this sort of "what is human" thing for years. Most shows like this are basically televised versions of what have come before. Even Star Trek was... er... I don't know, derived is probably the best word... derived off existing written sci-fi, and many major sci-fi authors wrote episodes for it. Which is why it was a classic. Galactica isn't the first to raise the question, and it's not the best story of its kind out there.
Galactica completely ignored the "what is human" theme later in favor of a "don't persecute" theme. It tried to make it interesting by going "don't persecute your creations"... but... they're just people who can stick wires and stuff into their bodies and upload their personalities into clone bodies, so it comes off as more of "cycle of revenge" story, which while relevant, isn't exactly high concept stuff. It seems cowardly (but expected to be palatable for a television audience) to make the Cylons completely like humans near the end and present that as the only right option. Why couldn't the humans have become more Cylon like? Could the Cylons only become acceptable by being absorbed into humanity by becoming more human? Does assimilation only have to go one way? I wouldn't mind how the show had concluded if they had even raised these questions. Instead they ignored it in favor of characters, which isn't really bad, but it's not what I like.
(They don't even keep the cloning bit, they just decide to go with what God wants and start breeding like normal people. Way to go Cy-humans.)
Cavil was totally right in that case, hell he even had an awesome rant where he tells somebody that "dude, why did you make me suck so much when you could have given me senses that could see into the ultraviolet", a question which could have been interesting if they handled it correctly, but no, he had to be malicious and evil and completely unrelatable.
What does "naturalistic" even mean anyway? I think you mean the first two seasons. The last two went completely overboard with the mystical elements, even making it part of the technology they used.
This is why I like The Sarah Connor Chronicles so much. The show has a fair amount of flaws, but at least it tried to handle the problems in integrating AIs and humans instead of sweeping it under the rug.
