It's going to take a while, but they are definitely going to keep moving in that direction. I think it's safe to expect future versions of Windows to continually de-emphasize and virtualize the desktop (much like what they did with DOS). Remember how they almost didn't release a version of Visual Studio Express 2012 that could target the desktop?
If they do this - and they have always wanted to - it will open the door for massive development on other platforms. I say this as a Microsoft developer. After looking at what's coming, both in the mediocrity of the upcoming OS releases and the push to put everything behind a MSFT wall, I've been actively looking at whether we should be moving primarily to Linux.
Document formats don't seem to be a problem any more. Back when MS switched to .docx people I knew continued using .doc to maintain compatibilty with old versions. I actually got support for the 2007 formats before most of my windows using friends. As long as you change your default file format to the MS one, I don't think you'll run into issues on that front.
