the current situation with the 2600 being faster with "pro" apps is a temporary one.
in every measurable technical way, the 8800 is considerably faster. it has a faster fill rate, a faster bus speed, more bus width, faster memory, faster gpu speed, more memory, and better on-board coprocessing for video.
the video features aren't currently being used by apple, but they are on the PC side, and they unload lots of things off of the CPU. there's no reason for apple to skip out on that stuff in the future, so expect support to come eventually.
there WILL be an updated driver for the 8800 that will address the speed issue wrt pro apps.
it is just a matter of time. of course, there will be a new 8800 for older mac pros, as well, and that's just a matter of time, too.
you never know with apple when they are just blowing smoke...