All the trucks (and cars) I've owned, and all the trucks my father has owned have been manual. Three 1 tons, two 3/4's and some smaller ones.
When I drive an automatic car (not very often) one of the first things I inadvertently do when approaching a stop is slam on the brake while looking for the clutch pedal. They make the brake pedal so large it covers where the clutch pedal should be...
I don't think there is anything particularly wrong with modern automatics, in fact I'm quite impressed by the Allison 5 and 6 speed electronic ones.
But for now I really prefer a manual transmission.
That said I have intentionally used parts in my truck project with the idea of easily switching to a 3000 Allison if I ever want to in the future.
Grigg