Automatics have come a long way since jeep started putting them trucks, (might have been the first manufacture to do that) As mentioned the auto gives you a measure of control at slow speeds and a place in the drive train that allows for some slip to absorb drive line shock loads but that slip, before the torque converter "locks up" creates heat, the fastest way I know to kill a slush box is to get it hot and burn it up. It is important to keep in in temperature so look into a transmission cooler and a honest to gosh temperature gauge to monitor it. If you hit the tranny case hard enough against a rock, the aluminum cases have been known to split like a egg, I have also seen the tranny pan ripped open by not only rocks but the front drive shaft. The result of these disasters in a dead vehicle, autos will not function with fluid escape. Most auto-boxes give a gear reduction around 2:1 or so but you have the fluid slip in the torque converter to make up for it. This kind of damage is on really hard trails though and not real common until you start doing those a lot, but it is something to keep in mind.
A manual has some advantages too. First among these is compression braking, the braking ability of the engine when going down hill. Some manuals, usually the earlier truck types are cast iron or cast steel cases, (newer stuff is the same aluminum cases auto have, foolishness) they take abuse a lot better than aluminum. Depending on the transmission some manuals are extremely strong and even if they do fail, or the gear oil is absent for some reason, they can be limped out to the trail head. However, with a manual transmission your ring and pinon gear and transfer case gear choices are much more important, often much lower than you would add to a auto equipped jeep adding a lot of expense to a build. With a manual transmission, in my opinion, a clutch is used for one reason, changing gears, I am NOT a fan of speed control through clutch, it just tears up your clutch and often the vehicle will surge ahead suddenly, especially if you have a habit of slipping the clutch. It is much better to choice the appropriate gear in the first place, let the engine idle and if you need to go slower apply a little brake to add some resistance to lug the engine down. This is a art and it does take some practice juggling clutch, brake and throttle with two feet. A wise man said "Keep you foot off the %$$^^ CLUTCH unless you NEED IT".
It is really, as mentioned what you are comfortable with.
