The problem is .NET won't solve the problem - there are tons of widely used legacy libraries/applications that are not 100% .NET (and often containing 3rd party binary blobs or DLLs that need to trickle down first) so it will take several years to migrate to such a setup.

Not to mention the massive confusion which would hurt MS real bad - imagine you have a certain version of Photoshop or AutoCAD you paid serious money for. Would you expect that suddenly you need to take care WHAT edition of windows do you have to run a certain application ? One of the reasons cited for the relatively small Linux netbook market share is that people wanted their existing/familiar apps and layout. Sure, the next major versions of those might support ARM but that won't help your existing software, and MS can't force 3rd party companies to upgrade you to the ARM version for free.

So the bottom line is - it's not Microsoft per se that is the barrier to ARM, but the application ecosystem that was nurtured in the (near) eternal backward-compatibility promise.