Auto works well for technical rock crawling tight trails etc where rolling back an inch can put you upside down or into a tree. Also is good for multitasking such as drinking coffee, talking on the cell phone, cb etc..
Downsides to the auto I have noticed are poor controls whether they be computer or shifter related that won't let it shift into the right gear at the right time, lock the torque converter etc. my XJ has the1-2 position together and without a mod you cannot manually control between the two gears and for the most part it defaults to 1st. This is annoying for fs roads and trails where 2nd gear would be perfect but it won't allow it and 3rd is too fast. Other example is my 06 CTD, stupid thing will not lock the torque converter in 4th gear until you hit 50mph, which is annoying on my 45-(50 if lucky) mph commute. Other example where I dislike the autos is shifting down on hills, I find my CTD unnecessarily shifts down, where it would have no issue continuing up over the grade at its engines peak in the torque curve.
Those examples given, I have been able to learn how to manipulate my driving to trick the tranny into where I want it to be performing but it isn't flawless and a manual would eliminate these complaints altogether but at the cost of drinking my coffee after leaving the coffee stand before I get up to speed...
As far as durability I really think its case by case. Seems I hear a lot of complaints about clutches going out, throw out bearings failing, flywheels warping, linkages failing, mc/slave cyls leaking failing etc. it just doesn't seem as fool proof as most say. Not that autos don't have issues and when they do its a complete replacement but just doesn't seem as frequent to me. Some autos suck, some manual boxes suck, still think its case by case.
Manuals have an upper hand in engine braking, speed control and efficiency. I would love to have one in my CTD. In older vehicles before autos came up with overdrive and locking torque converters I wouldn't even consider an auto over a manual in almost any situation. A lot to be said for not needing a computer to make the transmission work too.