The main reason you lose hardware acceleration is that the virtualized machine doesn't actually have direct access to the hardware (mainly the GPU). When it writes to the virtual "video card" it is in fact addressing the VM software. The VM itself is generally told (by the VM software environment) that it is running on fairly generic hardware without acceleration, and uses plain-jane video drivers.
There might ultimately be ways around this with clever use of CoreImage and DirectX type technologies, but this has been an issue with this kind of software since the beginning.
But I still think that a virtual system will be more useful for a majority of the applications out there. At least any of the ones I think I might need to use. I guess for gamer's a dual boot is the best option.
Besides gamers, CAD users (a group who have long been neglected on Macs) would greatly benefit from native performance on raw metal. There are also other technical apps that require good 3D performance besides games.
