[decryptthis_NSA]

Microsoft then bought out Skype even though it was clear it was non-profitable.

Lots of non-profitable companies are bought all the time. Skype had hundreds of millions of users and now Microsoft is urging users to make Bing as their default engine when upgrading Skype (just one example). Of course it can also be integrated for Office users too so that angle is not likely.

Do you have the dates for the switch? IIRC the previous owners joined PRISM before Microsoft bought them out.

Another thing: Microsoft needs to be in the good graces with the US Government, so does Google and to an extent Facebook. This NSA thing is quite popular for a reason or another among different senators, politicians and people that know know people. Piss them off and bad things could happen...like FTC, DOJ and IRS investigations.