Err what? All the apps still run and run natively. This not even like Apple's move to Intel. It's just the Start menu UI that's being changed. This is more like the Ribbon UI being introduced in Office 2007 replacing the traditional toolbar.
There were predictions then that companies would shift to OpenOffice because the ribbons were too jarring to users. How did that turn out?
My point was that the comparison must take into account the culture each company takes toward accommodating the needs and tastes of legacy/long-standing customers. Pulling out one example - the Ribbon in Office, which people still bitch about to this day, mind you - does very little to argue that Microsoft has a tradition of bold changes breaking existing user expectations. Such an argument would need to be much, much stronger.