Now that I’ve said that, I do want to make it clear that I haven’t seen an excellent exemplar of flat design. I remain optimistic though.
The single largest problem is that when we took 3D buttons away, we got no icon for the idea that you some object is clickable. An icon does not need to be skeuomorphic, just unambiguous and easy to recognize, besides, it needs to exist to be useful. Flat design uses a high-contrast background to encode that, what is extremely ambiguous, but there's nothing prohibiting people from creating a better icon.
Option this, Ctrl that. Yes, they can be discovered socially and informationally, but that goes against intuitiveness.
Simplicity goes too far on the balance of, and in search for, advancement of design. Form + Function. Not an industrial beige box bucket of parts and not a confusing 2001 monolith, but something in the middle.