These monkeys seem to have adapted quite well to their surroundings, eventually becoming apex predators. Their descendants were forced to venture out of the caves (obviously preferring to do so at night) in search of more and larger prey to satisfy their larger, stronger bodies. I believe that the long arms, dense musculature, and thick loose skin of the skinwalker are adaptations designed to aid in the snatching of bear cubs and mountain lion kits from their dens, and that skinwalkers are capable of fending off angry mothers long enough to get away safely if caught. It's also likely that their advanced vocal systems came in handy for mimicking the sound of mama bear to lure the bear cubs within snatching distance. Anyone who knows what a howler monkey sounds like will see how the skinwalker's early ancestors were able to mimic bear sounds, and from there their vocal systems kept on advancing until they were able to imitate a number of animal calls, including the screech of the mountain lion, which will account for the "unearthly" screeches so often associated with skinwalkers.
About 33,000 years ago, a new species began to populate the caves of North America. This new species was one which the skinwalker was already well-equipped to hunt. These new creatures were similar in size to bears and mountain lions, yet considerably less dangerous if they could be caught alone and unarmed. These new creatures, of course, were humans. Skinwalkers took a natural preference to the hunting of humans, and it wasn't long before they figured out how to imitate the human voice. The imitations were no doubt clumsy at first, but it seems to have been enough to arouse a fatal curiosity in those primitive humans, because over time the skinwalkers kept getting better and better and mimicking the sounds of human speech, with their vocal systems eventually reaching the level of complexity of the modern species.
I doubt that skinwalkers have a real understanding of the words that they say. Most of the stories which mention skinwalkers mimicking voices despict them as simply repeating the words of others exactly as they heard them spoken. To me, this is the best argument for the skinwalker being merely an animal. If skinwalkers were of human intelligence or greater, as one would expect of a corrupted human/evil spirit/alien, they would certainly attempt the far less unnerving feat of luring their prey with coherent conversation. We humans, however, are always eager to anthropomorphize that which appears similar to us, as well as to satisfy our curiosity regarding strange happenings, so the mere parrot-like mimicry of the skinwalker is frequently enough for it to get its meals. Stories of skinwalkers being able to literally take on the forms of those whose voices they imitate are no doubt derived from the exaggeration of second-hand story tellers, or otherwise imaginations that have been over-stimulated by fear.
All right, that's the easy part out of the way. The skinwalker's humanoid appearance is derived from its descent from New World monkeys, its pale complexion is derived from its ancestors adapting to life in caves, its strength and resistance to damage are derived from a diet of bear cubs, and its ability to mimic voices is derived from its relationship to howler monkeys and its strategy of attracting prey. There's just one thing I can't come up with a good explanation for: the stench.