In addition to the points noted in other answers, there is a significant technical difference: bearings. Traditionally, Dura-Ace equipment with bearings has had much better quality bearings/races/cups/seals/etc. That appears to be true here as well. Look at the parts breakdown documents from shimano and you'll see a significant difference in the axle/bearing setup:
* PD-6800 \- 12 ball bearings inboard, 12 outboard with bushing between
* PD-9000 \- 17 ball bearings inboard, 9 outboard with needle bearing between
The bearings in the 9000 will live much longer and deal with intense loads better than the 6800. That said, the 6800 is a fine pedal.