It's not really up for debate. Look at the Monroney stickers. Today's automatics are achieving equal or better MPG than manuals in the same vehicles. There isn't nearly as much parasitic loss through a modern automatic as their used to be, there are double the gears, and the ECU can totally control operation. So, automatics are now more efficient than manuals.
And, for pickup trucks in particular autos can hold more input torque which is why the OEs have all gone away from manuals on the diesels. Ram tried to hold on as long as they could, but even then they would derate the Cummins if the manual was paired to it.
Still, I prefer a stick in my muscle cars so my Challenger 392 has a Tremec 6060. But I'll always take the auto in a pickup truck.