Lack of a little built in flash might be a plus because the little thing and all the support needed for it is gone and there is more space for better features. Most pros would be using a more powerful strobe because one can control the power of the flash and rotate the head for much more control.
How did the D2 control remote SB-800/600's before the SU-800 was introduced?
Both the SB-900/800 are capable of being either a commander or a master unit for controlling remote SB-900/800/600 units and can control 3 groups of remote flashes and not just the 2 of the D700 and SU-800. You might want to review the difference between the commander function and master function. The SU-800 can only be a commander and never a master.