I was never a big Skype user, but my understanding is that Skype relied on individual users serving as "supernodes" in a peer-to-peer distribution network for messages and calls. The Skype client's default configuration opted you into serving as a supernode, and this was a supremely unpopular move.
It was more than that- there were antidebugger measures. The node list was encrypted. Protocol obfuscated. Also people in skype network were nodes. The supernodes were dedicated servers.
