You can't "simply 3d or directx" the desktop, because that would break compatibility with all your legacy apps - they use oldskool drawing functions that will in some cases draw on the desktop themselves, e.g. when moving a dockable tool bar in MS office outside of the window rectangle. (On a true 3d desktop, Konfab, AveDesk etc will cease to function.)
Siwu's SprintWindow is the most advanced candidate to accomplish this, but you see how it depends on driver installation. That kind of remoting must indeed come from a driver or system level so that GUI utility functions (in User32.dll etc) are redirected to a DirectX surface and not directly written to the framebuffer.
You don't want to have each pixel rendered twice or three times to accomplish this.
The main problem here is the age of windows: It has evolved from 1991 16-bit ISA CGA/EGA with 512 KBytes SRAM over VGA/SVGA to the fanned monsters we have today. Drawing GUI stuff in these days were deliberately kept simple because of the cards could barely hold the video memory, so overlapping windows were redrawn each time they were unobscured. This attitude is not compatible with texture happy 3d sceneries and stuff. Note how the screen flickers when you switch from desktop to game even if both have the same resolution. Note that DirectX games generally don't support being played in a window other than fullscreen: The reason is simply that side-by-side of both drops performance severely.
I'd recommend focusing on the real stuff and leaving 3d issues to longhorn.
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