I had a 6spd SD and my OBS is auto. Both are interesting in their own ways. A properly built auto with properly setup tunes with a hot setting and a tow-setting will make you pooh yourself with how awesome that slug of an auto will run. My 6spd sd was great, and granted I dont do long-haul w/ 20k lbs like a lot do (in which case I'd prob want the 6spd), but for an all around truck... logging, hauling, deep snow, farming, fields, retrieving stuck'd people etc.... I LOVE a well tuned auto. No worrying about shifting, lugging, over-speeding etc... just put that baby in the corresponding tune to with what your using the truck for, put the pedal down, and let the truck do all the thinking. Not to mention, a well-tuned auto with a good VB and TC will run just as efficiently as a 6spd because the actuation of the torque convertor locks the tranny up into direct drive (ie no slipping torque convertor) just like a stick is....
If I were pulling heavy loads across the country, I would probably stick with the 6spd.