While you are correct that the 6.7 I6 was an upgrade on paper over the 5.9 I6 that it replaced, when it comes to the used market it is our belief that the 5.9 I6 commands a premium. The 5.9 I6 has a near-cult-like following in the used market place and commands a huge premium, much more than the engine that replaced it.
With all of that said, are you certain there is a $10k difference between NADAguides value and KBBs? While you didnt specify which Mega Cab (SLT, Laramie, 2WD, 4WD, etc.) that you have, I cant imagine that there is that large a difference between the values. Our Retail value for the Mega Cab SLT 2WD with the 6.7 I6 (before any adjustments for equipment or mileage) is ~$26k, with an average trade-in value of ~$21k. If KBB is $10k more or less than these they are just outright wrong. On the high end (Laramie 4WD) our values are ~$30k retail and ~$25k average trade-in.