It is really personal preference.
In REALLY hard technical trails, where you are spotted inch by inch, autos win. So long as you can keep a minimum speed where you are not riding the clutch then it starts turning into a challenge of driver skills.
I have always been a stick shift person. My last hard core trail rig (lockers both ends, 4.88 geared, lowered transfer case gears, suspension made from slinkys, etc.) I ended up converting to automatic. I was running hard trails, well beyond a stock truck could do. At times I needed to apply force without actually moving, auto wins. But steep downhills could be challenging. That torque convertor that multiplies so much torque going up suddenly goes to a liability going down. As much as it slips under load it slips the other way allowing faster wheel speed then engine speed. It took a LOT of mechanical gearing to hint at keeping downhill speed control.
Now that I quit going out and trying to find the next $500 part to break on each outing, Didn't enjoy a rig that was scary on the highway, something that was new and could run normal trails. I just got a stick. At 4 days old I had a trailer on the back, going up a forest service road, in the rain, lifting a tire from time to time (playing around to see what this thing can do).
The stick is very capable but does take a skilled operator. Letting the smoke out of the clutch can get expensive. The Pro-4x has this neat little feature that lets you start it in gear. Little jerky but very effective for getting moving from a tight spot without slipping the clutch. I am very comfortable in the abilitys of the MT. I will point out that I don't plan on doing any severe technical trails with it either. The biggest downfall to the stick shift is the clutch will not tolerate a lot of abuse. Since this is my daily driver I don't abuse it. I need it to get me to work the next day. Simple, avoiding abuse avoids problems.
So you do have to decide on just how technical you want to get? What are your abilities to drive a stick? I don't typically deal with heavy traffic so a stick works fine. I have driven in heavy traffic, for that I admit I am lazy and get tired of clutch pumping and would prefer an automatic.