I'm the original owner of my 1999 Tacoma 5 speed manual 4x4. I've never driven an auto off road. Here's some pros and cons I learned from experience and research:
manual pros:
excellent engine compression braking when going down hills
easy roll starts in dead-battery scenario
excellent gear and RPM control
Yes, slightly more power being delivered to the wheel over like-equipped autos trannys (I did research it once*, not a guess)
Very few people ever ask to borrow your truck if it has manual.
Cons:
I had to upgrade my suspension just to reduce amount of stopping and starting on bumps/obstacles; it was killing my clutch by requiring more clutch activity on the constants stop/starts. With better suspension I can drive over more of it without stopping or slowing, downshifting.
Dang near nobody I ride with can not drive stick, so if I'm ever injured, I don't have a back up driver for my truck.
Uphills can be nerve wracking for some stick drivers if you go from stop to start on a steep hill. I do it all the time and have zero issues*, but for some it's a skill set they never quite get.
*I've accidentally pulled it out of first gear during a steep up-hill climb- by resting my hand on the stick. The uphill angle put down hill pressure on my arm/hand, and it was just enough with a bump to knock it out of gear once. Scary moment when the truck started going backwards for a second.
Less resale value in some areas. Although some people do seek them out and pay more for them. So it can make it a bit of an item later. (My brother can't find a low mileage 2nd gen Tacoma 5 speed to save his butt. Easily 95% of Tacomas out there are pre-runners; the remaining few percent that are 4x4s are almost all autos.)
Auto Pros that I know :
Much easier to rock-and-roll between drive and reverse when trying to get unstuck.
Much easier to manage slow, intricate torque-heavy maneuvering without destroying a manual clutch.
Allows easy simultaneous braking and accelerating (for activating some lockers/LSD systems during wheel slip or lift)
Anybody can drive it in an emergency
Much easier to drive in stop and go freeway traffic
Easier to tow (although that can really put a lot of strain on the auto tranny over time-- get a tranny cooler, they say)
Cons:
If not maintained properly, theoretically more prone to maintenance issues like overheating, and shifting problems. I had one auto in a 1970 hot rod I built, and that thing was a nightmare. Today's tranny's I'm sure are much better!
not as fun as stick driving, as we stick folks like to say
Less precise gear & RPM control
more people will want to borrow the truck!
Much easier to sell an auto equipped vehicle
don't have to worry about getting a good clutch replacement job one day, a vanishing art.
*Last I researched efficiency claims in auto vs. manual, back in the 1990s, there was still the famous "10 to 15 percent factor" -- engineers spoke of auto tranny's losing about 10 to 15 percent efficiency over manuals due to auto tranny internal pump and the big power-sucking torque converter. No getting around this ever, I suspect; law of conservation gets in the way. If an auto version of a vehicle got better gas mileage, it was for other reasons like gearing or test conditions. Bottom line was that manuals deliver more power to the wheel, even if you don't notice it or it doesn't show up in the MPG. But a bad manual driver can defeat all of that, just like a clever auto driver can also sometimes.
hope this helps!