Microsoft's problem isn't inherent in having a 'flat' design. It arises because of their alternately uniform (outlook), and seemingly arbitrary (metro desktop), color, contrast, layout and font-weight choices.

They could conceivably shift to a design-language where those attributes could be used to hint at interactivity at least as well as a big shiny buttons.

I think they are doing the right thing by making sure that they get the fundamentals right and then they can add to improve.

That is hell of a lot easier than if you have to fight with a and already established strong visual hierarchy.

I would do exactly as they are. That seems to be the right approach for such a huge undertaking that this will be.