Other than a 12g saving in weight and the Dura Ace label, are there any further potential reasons to prefer Shimano PD-9000 pedals over PD-6800?
Edit: This question is specifically about pedals rather than general Dura Ace vs Ultegra comparison.
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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:
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.
I was amazed to recently discover the Dura Ace carbon body is 0.5mm narrower than the body on the Ultegra. This was discovered quite by accident. I have a carbon centaur equipped winter bike on which I have Ultegra 6800 pedals and a specialised roubaix with 105. So I decided to finally splash out on dura ace pedals to match the dura ace 9000 group set on my best bike. Immediately I noticed the instep of my cycling shoe touched the outside of the crank. On testing back and forth, this was not the case with either Ultrgra or 105 latest pedals. This was a puzzle, as you should be able to move seemlessley between the pedals using the same shoes and cleats. Turns out the body on the dura ace is narrower. I presume the extra 4mm long spindle dura ace option will right the wrong. Perhaps that is what it is for? I have large size 64 feet.
According to this site, the differences can be summed up in the following
As for the carbon pedal body, the 6800 design differs from 9000 through its use of short carbon fibers instead of Dura-Ace's long carbon fibers. Essentially, this is where the extra weight comes from. Additionally, the carbon has been molded with a machined aluminum sleeve that houses the two bearings in each pedal. The whole assembly spins on a stainless steel spindle, and the new pedals retain the replaceable stainless steel wear plate that sits atop the pedal body. Additionally, it supports the SPD-SL cleat for maximum lateral stability, while allowing a hard surface for your cleat to float against -- +/- three degrees.