I have always preferred a stick because I like to have more control of what the transmission is doing. I tow a lot and have no problem. I just try to not stop then have to start up again facing uphill. I think the key to towing is not using 5th gear on the highways. I tow all over the country at 70 to 75 mph and it takes a pretty steep incline to require a downshift.
Clutch jobs are usually needed if you keep the truck long enough but that is cheaper than getting an automatic rebuilt or replaced.
There is nothing wrong with automatics, most people prefer them especially off-road. My 69 Fairlane Cobra has an automatic and I like it. I have driven a Cobra with a stick and they are a beast to drive. Modern sticks are much easier to drive.
2002 FX4 Bright Red Supercab 4.0 SOHC, manual 5-spd & Tcase, 33" BFG MTs, K&N air filter, Modified air box inlet, Gibson SS cat. back exhaust, Bama flash, Hidden Hitch round receiver, Rear helper air springs, Electric trailer brake controller, Line-X bed liner, WAAG bar with KC lights and Wildernest shell.