Personal preference
This is a well-beaten subject. It really boils down to personal preference and the intended use of the truck.
I've had several stick-shift CTD's, both 5spd and 6spd. If I were to tow heavy on the highway 95% of the time with my truck, it would be a 6 speed. The ratio spacing is very good, and the trans is very heavy built. However the 6spd has syncro issues, and is not a nice shifting trans, pretty notchy and takes a bit to get used to [if ever]. The shift pattern is for towing heavy, not for around town driving. [1st/reverse location]
If I had to have a stick and drive it around town, it would be a 5 spd. They shift much nicer than a 6spd, but the ratios have gaps, and the fifth gear spline/shaft issue is expensive to properly and completely fix.
Backing a big trailer with any stick with a strong clutch usually causes some grabbing and bucking, if I had to move trailers around a yard regularly it would be an automatic truck.
For off-road driving I would only consider an automatic. Try creeping over rocks and logs, easing over inclines with a stick shift, you are slipping the clutch constantly, this is what torque converters are for.
With a good aftermarket transmission you won't have any problems towing up to the weight limits of our trucks, and the vehicle is much more flexible for all uses, both around town and off road.
I describe my truck/trans as an automatic-shifting stick shift truck, The trans is that tight and controllable.
I set up my customers' transmissions for everything from mild to wild, set up for the use that the customer intends and to drive the way they want it to drive.
The cost of a properly set up auto is not much [if any] more expensive than a trans / flywheel/ clutch/ pcm /clutch pedal /steering column/ instrument cluster purchase and swap.
I Know that many people feel that the only trans for them is a stick, but I've had several stick-shift die-hards tell me that if they were to have an automatic, it would be just like the one in my trucks. A good aftermarket trans is that good.
The above are just my experiences and personal opinions, obviously others have their opinions and beliefs.
Greg L. The Noise Nazi