Here are a few observations after 9 years and 113k miles with a JKU with a manual transmission:
1. Rock crawling is no issue, whatsoever. Mine is a Rubicon with 4.10 final drive ratio, and 33" (really 33.5") tires.
2. I've had three problems with my transmission, two of which were typical enough that there were TSB's. First, I had a squeak at 18k miles. That was fixed quickly. The 2nd saw it popping occasionally out of 1st gear. I'd say this was somewhere around 60k miles, IIRC. They did some major teardown for this, but had it back to me quickly. Finally, the slave cylinder crapped out at 90k. I was able to drive it halfway across the country with no clutch, as the JK transmissin is VERY easy to speed shift. 300 bucks, and away I went, in about 3 hours. Yes, those were annoying problems, but none stopped me. I'm still on the original clutch, btw, and it feels fine. I've also done lots of towing. Not great, not terrible. As for driving, I've loved it.
3. 6 gears is plenty with the manual. With the 4.10 gearing, I've not felt the 3.8 has been as sluggish as my friends' JK autos. Theirs shift up and down, in and out of 4th gear, all the time. (I know the 3.6 w/ 5 speed Auto is MUCH better in this regard).
4. I don't have to EVER worry about transmission temperature or a cooler with a manual transmission.
5. The new JL reportedly will have a shorter driveshaft with steeper angle with the auto, as it is a longer package. This is an educated guess at this point, but it was by people familiar with the latest FCA auto transmissions. However, the manual is supposed to be a new unit, so we'll see. I'm betting it is a newer, stronger unit.
There is still a small chance I'll look at the auto. However, I love the driving experience of a manual, and it makes one **** of a theft deterrent, as statistics show a FAR lower theft rate becasue thieves can't drive them. :wink2: I also don't mind saving a thousand bucks, either.