I'm not sure why the accent on "Stop using MS, it's spying on you!" is on MS. AFAIK every company is using your data and giving/selling it to the government.
If someone drowns 4 kittens and you only drown 1 kitten, you're still pretty evil. I don't see how "everyone else is doing it" is possibly a valid argument. Obviously 'evil' in this case is based on your definition though, it's not exactly a universal concept.
Microsoft has been moving Skype from its original peer-to-peer architecture to a more centralized system for some time. After the Snowden shitstorm, critics have been implying that the move was NSA-related.
I might be wrong, but wasn't skype's p2p system used mostly for udp hole punching? (i.e., the supernodes were used to initiate the connection and then the clients communicated directly with each other.) With the centralized system, do the call contents go through microsoft's servers now? (this should be pretty easy to prove, doesn't it? Just check the addresses where your UDP packets are being sent to and received from.) It just seems to me that if anyone wanted to spy on you, forcing someone else to migrate to an entirely new system would be massive overkill: Applebaum's talk shows there are _plenty_ of better tools available to get to your packets.
EDIT: This really seems like an interesting question: _are_ there any advantages an attacker would have with skype's centralized system that they wouldn't with their previous p2p system? From what we've seen so far, I think the differences (from an attacker's perspective) are trivial.