One of the things I've recently (today) found out about Skype is that it uses a peer-to-peer protocol. For me that has two issues - 1) I don't know where my voip traffic is being routed through. Even though it is encrypted, that encryption has been compromised before and probably will be (if not already) again. And 2) while your Skype agent, app, whatever, is active, some of your network bandwidth is being used by others for their communications.
I only found out about (2) after re-installing Skype and noticing the number of firewall rules that were required just to get to the log in page. There was nothing in the installation process that warned me about the p2p protocol although it is probably buried somewhere in the depths of their T&C's also, I pay quite a lot of money for my limited broadband plus my ISP reduces my bandwidth if it detects that I am using any kind of p2p protocol.
Having said that, I haven't had chance, yet, to check to see if Apple's Facetime also uses the same protocols or not.
P.S. +1 for a Windows Facetime agent