The SU-800 makes you more efficient, as it's right up there and you don't have to dig through your My Menu to get to it. I use RPs most of the time now so IDK about the range differences between them, but I've read in at least a few places that the SU-800 has more range and power than SB-800's and SB-900's in commander mode, so I guess Nikon pimped it out a little to make it more attractive.
distance is usually not a problem for me. where I have issues is, sometimes I have my speedlite sitting behind an umbrella, 90 degrees to the right or left of the camera. That doesn't always work too well.
The more power you've got, the greater your chances are of getting the signals bounced off a wall or through your umbrella or to be able to use it reliably outdoors at noon.
The inbuilt flash will contribute to the exposure which can be a problem (unless you use a really strong IR filter on it). Shooting in a studio it is less of an issue but if you shoot in a dark environment and are using high ISO then the commander (even if set to --) will be the dominant flash. If you dont believe me, set the camera to iso 1250, f2.8 and try it. Try shooting like this with your main flash off and you will still get a decent exposure. The other advantage of the SU800 is that it is simple to set and that it has an AF assist (a proper one not that dumb white light)
The SU-800 is so much faster if you need to work quickly and the large auto-focus assist is nice. It's svery light so you hardly know it's there. As far as line of sight goes, that's one of the great things about the SB-900. Since the head swivels 180 you can turn the IR window any direction you want.
