The protocol and client are both obfuscated at cost to performance and security. Exploits have been found repeatedly for everything from remote code execution to using skype clients like a botnet.

Non-NAT'd nodes are forced to carry traffic for NATed nodes. Skype have the ability to intercept your calls, but you guessed that anyway.

Also, if everyone in the world used one phone company, or bank, and that company refused to allow other new companies to inter-operate, they would face antitrust. Skype, and arguably facebook, control their markets. They should be forced to allow inter-op.