* The nefariousness one: So Microsoft can let NSA and the cops listen in.
* Because mobile clients don't work well with P2P.
* Because servers and bandwidth got really cheap.
"An executable-only object code form of the GI Software was licensed by Joltid to Skype, a well-known Internet-based company that provides users throughout the world with free or low-cost telephone services over the Internet. Skype did not obtain a license to the GI Software source code, however"[0]
[0] - https://techcrunch.com/2009/09/18/new-lawsuit-brings-clarity...
Yet, dissonantly enough, this is exactly the model you accept if you use proprietary drivers on your system. Arguably, it's the model you accept if you use any proprietary software - programs are not perfectly isolated from each other.
If you found this revelation about Skype to be vaguely shocking, as I did, consider if your reaction is consistent when it comes to the other things in your life - like your Android phone.