Protocol is closed and little progress has been made for reverse-engineering -- which I think would also be illegal, since the data is encrypted and then you're at odds with the DMCA (IANAL btw -- the DMCA grants a safe harbor for reverse engineering, but that hasn't worked out so well for DRM).
To my knowledge there is no alternative Skype client, not even for the IM part -- Pidgin has integration with the official Skype client and piggybacks on top of it. If you don't have the Skype client installed and running, Pidgin doesn't work.
P2P in this particular case is really not the freedom-giver technology that allows you to workaround Skype's servers. If Skype wishes to serve adds to you, or to track you, there's really not much you can do about it.
I believe the DMCA outlaws circumvention of copyright enforcement mechanisms, not encryption. I don't see why the Skype protocol would have any such mechanism.
Looking at how complex it is, and considering that Skype probably have more obfuscation and crypto ready to roll out if anyone cracks it, I can see why nobody's implemented a compatible client:
Edit: this is pointed out in the linked slides.