I have had both automatic Jeeps and a manual Jeep both had stock 4.0l engines. I had a great time in both. I used the manual when off-roading more and the Auto as my daily driver in heavy traffic. The off roading I did was not sand or dune based. So I am following this thread to learn more. What I did like about my experience is having that second vehicle, if one breaks (Usually the off-road one) you will have a second car to get to work at the end of the weekend and until you get one fixed. Doing it again I would buy a Jeep with better lift, wheels, lighting, and everything else that I want, that is in my budget. The type of transmission is lower on my priority list.
When I was young, 30 years ago, I would kill car batteries a lot. Dead batteries of the past still haunt me. I have not killed a battery in 2 decades. Since those time being stranded still haunt me if I found two Jeeps that are equal I would probably get the manual.