I would say the best practical reason to move over to a flat design is performance increases. It has been shown that CSS properties such as background-image gradients and border-radii are among the worst offenders for decreased front-end performance. With websites approaching 2MB in size it is no surprise to me that flatter design makes for smaller files (less CSS prefixes, less JS repainting) and less browser rendering. This was precisely why our company moved over to a flat design as we've increased the number of users rapidly over the past year.
You're falling into the trap of thinking everything is HTML. This doesn't apply to native code. There's very little penalty for using rounded rects, drop shadows (which are part of most drawing primitives), and gradients.
