"Once upon a time, all UIs were flat"
Did they really go with the '3D' look for buttons because of usability studies in the 80s? Or was it because they wanted to show off the computing/graphics power they had and make flat buttons look dated and backwards? I'll bet it was the latter. Apple seemed to be the only company that ever gave much credence to usability studies back then - if Microsoft paid attention to them back in the 80s and 90s they need their money back!
Once everyone and everything had 3D buttons by 2000 or so, I guess Microsoft decided to be different and unfortunately for the rest of us Steve Jobs liked what he saw. He always liked simplicity, so I guess its not surprising, but too bad everyone else went that way too.
Maybe it is like hem length, and everything that is old will become new again. The old flat buttons rule today, but maybe soon we'll see the 3D buttons return in a UI here and there as a way to stand apart from the crowd, and it will come back into fashion.