So, the Colonies can build cylons, master galactic travel, but can't make a good prosthetic replacement leg?
Well, they don't exactly have the full range of technology they had back on the Twelve Colonies with them. They have what was aboard Galactica and it's fleet, and they salvaged from Pegasus before it was sacrificed. Galactica was being decommissioned and was technologically backwards to begin with, so I doubt it would have just happened to have state-of-the-art prosthetic limb facilities.
For all we know in pre-holocaust Caprica they could have given him a mechanical prosthetic that was almost indistinguishable from his original limb.
Onto the issue of the episode itself, looks like the Cylons really are a lot older than we give them credit for.
My theory, convoluted but fully fitting the facts is that:
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Human life originated on Earth, many, many millennia ago. IIRC Bill Adama's personell file in the episode "Hero" showed the year as being around 21311, so it's clearly the very distant future (the 214th century).
Somewhere in our future, quite probably many thousands of years from now, humanity left Earth to settle on Kobol for reasons unknown, such as some cataclysm that made Earth uninhabitable.
The Cylons were originally created on Kobol, thousands of years ago, after thousands of years of civilization on Kobol to the point where Earth was at best a distant memory, legend or trivia question as the origin of Humanity. Then the Cylons developed to the point of being cyborgs, and eventually biological. The human civilization dealt with the societal strains of having a race that was created as mechanical servitors, but now were fully sentient organic life that could only be distinguished from humans by detailed medical examination. Eventually this lead to a civil war on Kobol. By the end, Kobol was uninhabitable and twelve nations of Kobol left for new worlds to settle on, each lead by charismatic figures that would be later known as "Lords of Kobol". As the humans were going in one direction, the Cylons went in another. With Earth already being probably over 10000 years ago in human history, it wasn't hard for them to think of Kobol as their home and Earth as only the place where the "13th tribe" went to.
The humans found a star system and made it their own. Using their highly advanced technology (remember, we saw them with practically holodeck-like technology in the ruins of Kobol in Athena's Tomb), they terraformed 12 worlds and created 12 nation-state worlds, each as a separate sovereign entity.
The Cylons returned to Earth and decided to resettle the world that had become habitable again after millennia. They created a life very much like human civilization (from the few flashbacks we saw last night). We don't know why or how, but something lead to nuclear detonations throughout Earth. Massive, and very dirty detonations that killed virtually all life on the planet and even 2000 years later left detectable levels of radiation in the environment that made long-term habitation impractical.
To ensure their survival, the Cylons had enacted a master plan that would take over 2000 years to come to fruition. For unknown reasons they left the marker beacon we saw earlier, and built the Temple of the Five as another marker to Earth. Then, they arrived at the Twelve Colonies of Kobol, and somehow planted the seeds of their own technology so that humanity would recreate the Cylons. Once activated, complex sets of hidden directives and memories were loaded into them by the Original Cylons so that they would recreate their former civilization. Unfortunately, the only way the Cylons could develop that kind of biotechnology to recreate their old forms would be to do things humans would probably object to. So, the Cylon Wars broke out so that Cylons would be able to capture humans for experimentation and work on their own development unimpeded by humans, so they could create bodies for the personalities of the old bio-cylons of Earth to download into.
We saw in Razor that as soon as the Cylons had a functioning Hybrid and were well underway with the development of their biological models they called off the Cylon war and fled known space.
Once this had been executed, the Cylons were on their own. They didn't have full knowledge of who they were, or where they came from. They didn't really know why they had five of twelve models that were sealed off from their collective, they just knew that some other, outside entity had been guiding them and they treated that as divinity.
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As for Starbuck? Who knows. Maybe the Cylons cloned her somehow, and she's not a cylon but was recreated with her technology. Must be pretty fraking harsh to find your own charred corpse (with your dog tags) sitting in the wreckage of the vehicle you remember disappearing in (with matching serial number). The gamer in me is wondering how much Sanity Loss that would be in Call of Cthuhlu.
