Basically, insert classic XKCD org chart diagram here of Microsoft being in a Mexican standoff with itself, especially at that time.
From that perspective, (and also one of being a Windows Phone 8 and now 10 owner), I don't think Skype was bought for Windows Phone and I don't think Skype is part of why Windows Phone is currently seeming rather atrophied. Instead, I think its Windows Phone where we've seen some of the hardest fought "battles" in the "One Microsoft" movement to de-escalate the old "mexican standoff" at Microsoft. (Which makes sense in a strange way: Microsoft couldn't afford as many "casualties" on the desktop or in the enterprise, so phone/mobile has been the proxy war.)
I think wanting a VoIP competitor to Apple's Facetime efforts was a part of the overall agenda for at least one of the messaging teams. But in terms of a lot of the shifts in branding choices and app approaches, I think a lot more of what we have seen in Windows Phone has been Microsoft's most externally visible battlefield where it has been trying to figure how best to merge all of its messaging and communications teams and destroy the old fiefdoms and silos (and guns pointed at each others heads). (All while marketing tries to fight from accidentally burning down a brand along with some of the bridges...) Windows Phone was just a useful catalyst (battlefield) to force that confrontation, without impacting the desktop too much.
That's essentially what this announcement seems to be about to me: the crashing down of another silo as Microsoft truly starts to consolidate its many communications apps.