In the first book, Darkly Dreaming Dexter, Dexter wonders if he might be killing people as the Ice Truck Killer in his sleep. One possibility is that the writers decided to run with this and since Dexter experienced the thrill of a new, outside of the code, kill he's been skinning people in his sleep.
Also, remember what Dexter said at the end of season 2, about the "need to explore new rituals." So far in season 3, he's followed the same basic manner of killing/dismembering people. The skinning would be his first real step into a new ritual.
This would also be something new to the story as the only current suspects are cops and Deb's love interests, which would be predicable and pretty uncreative since the first two seasons went there already.