1) smaller size (not just for portability; much more manageable atop a carbon fiber tripod) 2) Built in CLA. Not having to fiddle with the SU-4 is nice, and the in-camera controls work great 3) Grid lines in the viewfinder. Useful for aligning architecture shots.
If I were a different kind of shooter my list would perhaps favor he D3 - astounding battery capacity, giant bright 100% viewfinder, bullet-proof body, faster frame rate, more durable shutter, body form factor. . .