I'm the author of the original article and I'm happy to receive e-mail at my EFF address (as another commenter pointed out, you can find my staff information page by clicking on my name there).
The focus of my post is the legal uncertainty about why Microsoft may not be able to improve the cryptographic privacy of Skype (even if they accepted our view that they ought to). Microsoft's recent statement seem to suggest Microsoft thinks there are now (or will soon be) legal considerations limiting its ability to protect users' privacy.
I'm aware of the key exchange problem and, in fact, the (lack of a) way for users to verify keys is the particular kind of anti-eavesdropping protection that my article calls out. I don't think that the supernode architecture or Microsoft's changes to it necessarily made a major qualitative change to Skype's privacy properties. Microsoft made a blog post at the time of the architectural change, and again recently, denying that wiretapping was the motivation for the changes. It's possible that the changes made wiretapping Skype calls easier even if that wasn't the motivation for making them.
According to the 2005 report, Skype effectively functions as a CA for its users, but there is no way for the users to check whether the CA's statements are accurate.