There may be several reasons to why MS has spent billions on Skype purschase, but there is one that falls into a spectrum of an IT-person's iterest; and that is the technological aspect of skype itself. 

A short background into on MS technologies and what makes Skype so special in a list of facts:

• Skype is probably one and only app, who's protocol hasn't been cracked, custom endpoint applications to skype services haven't been created. So no one knows what's inside of Skype, what makes it tick. 
• Skype, dispite the fact, that Wikipedia claims that it has been written inside Borland Delphi IDE, is a masterpiece software.
• Skype API is very limited and buggy (at least currently), so taking it, and writing a custom application to introduce Skype functionality into it would not be a good idea.
• Skype is so fat a native application on all platforms. No Java-dependencies on Unix-based OS's, pure native execution in Windows.

So, the only company, that can make a good Skype client, is the Skype Corporation itself.    

• MS, besides Skype purchase, has spent at least a billion USD on a development of it's Windows Phone platform. Which is very good, by the way. 
• All the user applications in Windows Phone are managed code. Either Silverlight for WP, or XNA games.
• Managed code is immposible to debug-protect, at least to the extend that Skype protects int's client applications.

This concludes, that in order to bring Skype to Windows Phone, Microsoft would need Skype to break the rules and release an unprotected client. Of cause, they could have negociate a possible native integration with Windows Phone, but since MS would be an interested side in this conversation, Skype would probably ask for such development a fair ammount of money, even if in all, it would appear to be possible.

We hear that Skype is to be released this year on Windows Phone. I bet it's goint to be released as a system update, not a standalone application. But here you go, an important possible reason, that forced MS to purchase Skype - to keep a secret, and a mobile platform.