Microsoft has made some poor decisions in the past for innovation, but they do not make stupid business decisions. They did not acquire Skype to screw it up by pulling it off non-MS platforms, or fire the whole dev team or reinvent the wheel. The bought it for the user base and the technology. If they where to reinvent skype as something else entirely and screw up its multi-platform support or change the protocol, they would be undoing what they wanted to buy, which isnt a sound business decision..
And frankly as dumb as Ballmer is, Gates is still a powerful voice on the board of directors, which he is still on. He'd not go for another 8 billion dollar screw up such as the Phone of Windows, 7 windows phone, Phone 7 Windows--Pardon... WINDOWS PHONE 7..
As far as Microsofts ability to keep pace with the industry at this point, I think they went from leader to 3rd place. As both Apple + Google (pick your order) are both ahead of Microsoft for todays trends..