I might have a complete misunderstanding of the situation, but I see three main explanations: 1) Microsoft has absolutely no interest in Skype being a viable option, and wants Skype users to adopt some other Microsoft product. Why doesn't Microsoft tell Skype users "Well, Skype is done, just use MSN." 2) People responsible for Skype are optimizing for some metrics, which is opposite to user satisfaction. What is that…
"Why doesn't Microsoft tell Skype users "Well, Skype is done, just use MSN." I'm not aware of anything else they have now that could be supposed to replace it? They already did this the other way around. They closed MSN Messenger in 2013, and told everyone to just use Skype. Skype WAS supposed to the their main messaging app now.
So in reality you might as well say they "reskinned" Office messenger, called Lync (which I believe started as a version of MSN messenger long ago) and then put out an "update" for Skype that replaced it with Lync, with the banners, window titles, website names, etc, replaced with "skype". That's what happened.