We have all been down this road. Whether in your buddy's garage, out on the trail, or over a pint down at the local watering hole, the question of manual versus automatic is an argument that has been raging since before the first Powerglide was swapped into a Jeep.
The pros and cons are pretty well known by now. A manual transmission offers anvil-like reliability that doesn't care what angle you run it at, compression braking that no automatic can match, and a much more involved driving experience. The automatic, on the other hand, makes rock wheeling so much easier and makes driving on the street a nice and relaxing cruise.
Despite knowing all of the pros and cons, we all still have our preferences. Your three favorite monkeys like to think that we base our preferences on facts, but the only irrefutable fact is that everyone's preferences have just as much basis in experience as they do in cold, hard facts. We are sure that Joe Friday is rolling over in his grave for this one, but enjoy our poo-flinging gearbox session anyway.
Trasborg Weighs In
Let me start by the one statement that usually makes people think I'm the old dog that can't be taught any new tricks: "My favorite transmission is the SM465." Then my bonus follow-up statement that further puts me out with the lunatic fringe is, "I just don't trust automatic transmissions and I try to avoid putting them in my Jeeps if at all possible."
Look, I know that an automatic can be built to withstand the abuse we put them through, but I've had so many die on me over the years and a few leave me stranded that I just don't trust them. So unless there are outside factors, I try to avoid them. About the only one I do trust is the AW4, which I have in my '98 Cherokee, and even then I will tend to take a manual-equipped Jeep out into the desert if I know I am going to be far away from civilization.
On the manual side of the fence, I have a lot of first hand driving experience with the SM465, AX15, AX5, NV3550, T-150, BA10/5 and T-176. I've had two Wranglers with the infamous Peugeot BA10/5 and managed to rack up over 100,000 miles on them without blowing a single one up. So personally, I've not had any problems with the transmission. The internal hydraulic slave cylinder is another story, though. That said, I've had enough friends and acquaintances blow them up with some regularity and have been involved in plenty of transmission swaps because of them that I wouldn't recommend the BA10/5 to anyone, but I wouldn't hesitate to buy a Jeep just because of it.
The T-150, while I've never blown one up, has such a stupid-high First gear that it is near useless in the rocks or really anywhere off-road. The T-176 is another one that has gotten a less than stellar wrap over the years, and while First gear is nothing spectacular, I still had no problems with it in my V-8-powered CJ-7 rolling on 35s for somewhere around 40,000 hard miles. I've blown up more AX5s than I can remember and the only thing I have to say about that is that if you have one and kill it, you should definitely look into swapping in an AX15.
The SM465 has a great granny gear, I've run a couple of them with no oil accidentally, and they just take abuse. Sure, very abused ones can pop out of gear and almost all of them are rough to get into gear-but they are reliable. The AX15 and NV3550 are just about interchangeable to me. The NV3550 is probably the stronger of the two and has a better First gear, but I've got somewhere north of 500,000 miles on only three different AX15s and that seat time gives me a lot of confidence in them. The NV3550 always makes noise even in Neutral (which can't be good), and it takes expensive gear oil. Sure, I have about 40,000 trouble-free miles under the belt with one, but for the premium price they command over the AX15 I have trouble sending people that direction. I'll always say, "Well, find an AX15 or an NV3550." The external slave-cylinder-equipped models use all the same bellhousing and clutch stuff, and even the internal hydraulic throwout bearing versions can be easily converted. So to me the real questions are "What condition?" and "How much money?"