The best trany? one of each!
I have two CTD's, both '94s. The dually was ordered as an auto, I bought the 3/4 ton as a 5 speed. I have since swapped the trannies. The Dually was hopped up to 230hp before swapping, and remains so. The 3/4 ton is still stock.
I pull a gooseneck at roughly 19,500# GCW (gross combined) I went thru the original auto and one rebuild before giving up and going to the stick. I believe that I ended up in a reduction in performance, but an increase in reliability by going to the stick. There is much to be said about the loss of boost during a manual shift, both for play and towing. Ultimately, I think I will be able to boost the HP to compensate and still maintain reliability, but it will cost additional money. Power braking is a thing of the past now that I stir the gears myself.
I did the swap shortly before the ATS TripleLoc convertor showed up on the scene, and have ridden in two strong trucks that use them. One is a fellow club members '98 12v, the other is a co-worker's '01 24v. One pulls a gooseneck like me, the other primarily drags, dynoes and sled pulls. Based on what I see of these trucks, I would not have switched to the stick if I had it to do over. Stock convertors are the weakest part of the drivetrain, but the aftermarket, especially ATS in my opinion, have really improved convertor technology.
I'm a flatlander from the Midwest, but I recognize the advantage the stick has when coupled to an exhaust brake. There's also no T. P. S. to hassle with. Also, I do have a P. T. O. hydraulic pump used for the dump hoist on one of my goosenecks that would be a tougher to acomplish with an auto transmission, mounting to the P. T. O. on the transfer case would not be as user-friendly.
So, bottom line, like nearly everyone else has said, it comes down to your anticipated usage and priorities.