Well here's a couple of reasons:
1. No 3D OS to date has ever been successful, people just don't know how to inovate anymore like they used to...
2. It would make computers a lot more expensive since a higher demand would be put on GPU's and they are pretty expensive compared to crappy integrated cards.
3. The cost to develope a good one would probably be insane compared to a conventional 2D OS.
4. No one has any ideas as to what advantages a 3D OS would have...it would probably be harder to navigate since a Z-axis is used and modern mouses would need a new buton or something to use that Z-axis effectively, therefore making development costs even higher, and how would that new button be integrated into the mouse so that someone new to computers could pick it up and use it without a manual?
5. People are stuck to the 2d OS enviroment, a change would mean more learning, just remember how pissed people were with Vista's new enviroment...imagine how pissed people would be with Windows 3D.
Hopefully that will shed some light on your question. But then again maybe you can be the one to invent a 3D OS lol.
6. To take full advantage of a 3D OS new programs would need to be created and guess what that means? More development costs. All the default Windows programs (assuming Microsoft created this 3D OS) would need to be redone, meaning a new Internet Explorer which is probably the most important, a new Windows Media Player, a new Windows Media Center and a new everything.