Well that's probably at least in part because a major motivation for that acquisition was not to actually improve the underlying technology. To quote verbatim one of my favorite hn posts of all time (https://news.ycombinator.com/item?id=18411779):

  A series of headlines:

  2009 - NSA offering 'billions' for Skype eavesdrop solution [1]
  2011 - Microsoft buys Skype for $8.5 billion. Why, exactly? [2]
  2012 - Skype replaces P2P supernodes with Linux boxes hosted by Microsoft [3]
  2013 - Microsoft handed the NSA access to encrypted messages. Subhead: Skype worked to enable Prism collection of video calls [4]
  
  1. https://www.theregister.co.uk/2009/02/12/nsa_offers_billions_for_skype_pwnage/
  2. https://www.wired.com/2011/05/microsoft-buys-skype-2/
  3. https://arstechnica.com/information-technology/2012/05/skype-replaces-p2p-supernodes-with-linux-boxes-hosted-by-microsoft/
  4. https://www.theguardian.com/world/2013/jul/11/microsoft-nsa-collaboration-user-data

Here is a series of headlines that give the best explanation of this architectural change that I've ever seen:

https://news.ycombinator.com/item?id=18411779