Like most things, it depends on what type of wheeling you do, and mostly personal preference. For rock crawling a stick can work nicely if the gears are low enough, but they need to be real low (t-case and rear end), while an auto works well without needing such low gears. You can't even think about doing serious rock crawling with a stick if you don't have low t-case gears as well as low rear end gears.
I prefer an auto, as do most rock crawlers. Nearly all comp rigs are autos. I wheel with a number of friends who had sticks and swore by them, but then ended up with a rig with an auto, and now they'll never go back to the stick. I also have plenty of friends who wheel hard and swapped out there sticks for autos.
You'll find those who are happy with manuals, but the vast majority prefer autos.