I realize that we can still use the desktop, but my experience has been that it is more difficult to deploy .NET applications on Windows 8 than at anytime in the past. Just the fact that it took us 4 weeks to figure out how to automatically activate .NET 3.5 on a Windows 8 system that does not already have it activated is ridiculous. To me, this points to the fact that the desktop area is entering the legacy phase.
You must not have tried side loading for your Enterprise yet. You will change your mind on what is easier (Windows Store App side loaded versus desktop on Windows 8).