I notice that "flat" icons and buttons lack robustness to unexpected changes in visibility or composition. Take a pale single color shape without an outline and put it on a background of uniform color and it will likely disappear if both colors are similar enough, or have same luminosity. The outline or the shadow of a 3D icon with multiple coherent layers would still remain visible, so the icon can be read from the fill or the line, whichever works. A color clash commonly occurs if you look at an LCD from an angle, or with icons that can be freely arranged.
Another vote for beautifully designed BeOS icons, or the similar ones from Windows 98/2000.