I've heard of some using the hand throttle to wheel, but myself I never use mine for anything but keeping the revs up while I'm running the air system or welder. I do remember one time when a buddy was letting his wife drive on the trail for the first time. She stalled it on a steep hill and pretty much was in a panic state. He just had her restart it, and let out the clutch while he ran the throttle from the passenger seat.
I think for competition Jeeps, the auto is without question the way to go. Much smoother application of torque. The auto is more forgiving on the drivetrain too. Autos seem to hop less.
But for me, the manual is the only way to go. I like the downhill control and my crawl is low enough it makes up for the advantage the auto has in most aspects. Plus, I have a trail Jeep, not a competition Jeep. And a trail Jeep's priority is reliability. If your starter dies, you simply need a push start.
This debate has been going on for ages and it always just seems to boil down to what you like.