I'll tell you the story of my friend Greg.
Greg has been a believer in Microsoft. He went to all the Tech-Ed conferences, attended every MSDN event he could. Conferences are grand stages that leave an impression. He drank all the cool-aid that was served at these conferences.
Things were really good early on, this was the last decade. The computing scene at that time revolved around Microsoft like the many moons of Jupiter. Greg and his team built products with Silverlight, WPF, .Net, Windows Workflow, Biztalk, Remoting, and the like. Every conference offered something new, something exciting. The apps they built worked great, looked great.
Fast forward to now. Greg is a decent programmer, but he wants a new job badly. The problem is that nobody wants to use all that stuff that he knows. People want to build on standards; apps that work on every device. Not just on Windows and not just on Internet Explorer. Greg still doesn't get it. He hasn't seen much of the world outside Microsoft, and still wonders why people don't want Silverlight. Still tells me how WPF is so much better that anything else out there. And running only on IE, why is that even a problem? Everybody has IE. Poor Greg, tough times.
There may be many issues with Microsoft. But more than anything else, I would fault them for building their entire ecosystem with total disregard for standards, their refusal to work with whatever community existed outside. This probably wasn't intentional, they must have probably believed in what they told their developers. Even though so much has changed since their glory days, there's a part of Microsoft which still refuses to engage.
There was a Steve Jobs interview from the late 90s in which he said, "The problem with Microsoft is that they have absolutely no taste". Jobs wasn't talking about aesthetics; it is true of pretty much everything from Microsoft. From UIs, to development frameworks, to tools, to shells and even APIs. Back then, having "no taste" was totally fine because people communicated far less.
Now we have a whole bunch of people who are stuck using this stuff. And many of them don't really get it yet.
Edit: I just saw that you work for Microsoft, and specifically Microsoft Research. You guys make awesome stuff. The above is mostly about the Windows platform.