Totally disagree on manuals being better for towing, in my opinion at least. Yes the automatic will heat up, but if the truck is below or at it's rated load then it's designed for that so that shouldn't be a relevant factor.
Otherwise you don't need to worry about shifting which should be a huge help. You don't need to worry about the clutch slipping if at an intersection or stop and go traffic, or if your on a really steep hill (hell you might even lose traction if you dump the clutch instead of slipping it, which results in the same heat as an automatic but it's not designed for it). And if you are towing livestock, you have to slip the manual to not bang the animals around, and that's even harder if you are navigating a trail to a trailhead with a trailer and need to creep around boulders. Lots of people claim that "you can control what gear and rpm the engine is out". I agree it's much easier yes, but you can control the gearing in an automatic just as much. There's a reason there's a shifter, you can override which gear the tranny will max out on if you want, otherwise the engine will be at the optimum gear and rpm.
Where I live, there are 10% grades routinely just driving to work. You will lose your brakes going down the hill once unless you downshift, and likewise if you are in a manual it's a b***h to accelerate up the hill if you have to stop part way up. As such, I don't see why some people think manuals are better for offroading, since you can't ease on the power as you like, you either slip the clutch or dump all the flywheel torque into the axles.
Is there just something that I'm missing that makes manuals better? I agree manuals are a much more efficient transmission, however a properly designed and used automatic is better in a lot of cases, especially for towing the kinds of loads our vehicles see. And you can't compare 18-wheelers to our 4Runners in terms of towing, it's like apples and oranges. Again, this is all just my opinion so please correct me if I'm wrong about some point.