From the Flat UI and Forms post at A List APart by Jessica Enders:
The problem is that in the push for simplicity, flat UIs may have gone too far. With content, things like drop shadows, gradients, and borders may well be no more than useless “embellishments.” When we read a multi-page news article, it doesn’t matter much whether the mechanism to move to the next page is a button or a link. With forms, however, distinguishing between a button and a link matters far more.
I am not a fan of pushing all design elements to be flat. When we use the same design style for all elements then the distinct features between different groups of elements is lost. One major victim of this is are forms and buttons.
We don’t do this in real life for the most part because it would only result in more confusion. Imagine if we designed door knobs to be exactly the same as the door itself. Instead of being able to easily identify where the door handle is, almost without thinking about it, each door would be a unique challenge in discovery because there would be no normal design clues that separate the knob from the rest of the door.
Making everything flat is the opposite of the don’t make me think approach to making things easier for people using your site.