For the OP. I recently sold my '06 5.9 and got a '15 6.7. I cannot speak to the early 6.7's. I loved my 5.9. I put a Pacbrake on it and that worked great! I had no problems what so ever with it. Sold it with 90K trouble free miles on the clock. It always had all the power I ever needed and I tow a lot. I would advise you to go 5.9 due to less problems and higher resale value. I had the six speed so I don't know about the auto.
Now the '15....this is an amazing truck; the level of refinement is amazing! Goobs of power, Aisin 6 speed, and so smooth and quiet. No real comparisons between the two trucks. DEF doesn't bother me at all.
I sold the '06 because I outgrew it. Short bed (upgraded to fifth wheel from bumper pull) sucked with the trailer clearance danger, and the the quad cab got way too small for my family...it really is a small passenger compartment for a 4 door truck. I sold the truck for very nearly what I paid for it new in 2006, but that was due to the 6 speed manual.