While I don't own a JK just yet, I've had 2 TJ's. The first was a '97 Sahara with the 5spd manual and 4.0L. The second was a '05 Unlimited Rubicon with the 4spd auto and 4.0L. Honestly, I regreted getting the auto within a few months of buying the Jeep. The main reason was highway driving was terrible. It was constantly searching for the right gear and would bog waaaay down going up hills and then drop into a lower gear and rev the RPMS way up. It was just a pain and the constant downshifting of the auto caused gas mileage to not just be bad, but really bad.

I live in Oklahoma and it is flat and windy in some areas and lots of hills in others so until Jeep puts a more powerful engine in the Wrangler an auto is just out for me. I've driven a couple of JK's with both set ups and the 6spd is the only way to go for me. After driving an '08 unlimited rubicon with the auto I knew I couldn't do it. It just felt too sluggish for me whereas the 6spd felt like I could at least get out of my own way and merge onto the highway without causing a wreck.

 

Manual all the way...

 

A manual for me is the best option. On the trail you have the option of selecting the right gear before taking on an obstacle. The perception that the slush box makes it easier on the trail does not hold water - you shouldn't be be changing gears in the middle of an obstacle or in the middle of a water crossing.

 

+1 Manual here

 

To each his own but for me it's a manual hands down. I've owned a 94 YJ with a manual, an 05 LJ with and auto, and now my 07 with a manual. I got rid of the LJ within a year because of the auto. It just never felt like a jeep to me.

 

The best transmission is the one that comes with the jeep you love and decided to buy!

 

I had an auto ZJ (first gen grand cherokee) with the 4.0 I-6 and 42RE combo as my first vehicle. After driving it for close to 10 years I decided that I wasn't a fan of the auto transmission in general (gear selection and large change in gear ratios between gears). I will say that for more challenging offroading that auto is a superior choice IMO. But I use my JK on the road about 99% of the time, so since I preferred a manual for on the road, that is what I decided on for my JK.

Whatever you choose I'm sure you will love it, after all it is a Jeep!

 

A manual is a blast in small light vehicles ,you are more involved in the "driving" Bigger,heavier vehicles that tow & do off-road work are better with the automatic,more control,torque where & when you need it,they down shift for engine braking nicely too.

 

I have a 2009 Mini Cooper - Manual all the way.

I had a 1991 Mustang 5.0L Notchback - Manual all the way.

2010 JKU - I went with the automatic. Much more convenient. For me, the manual felt like I was driving a big rig (that's comparing it to the Mini Cooper). I could probably do either but the automatic was a good choice for me. Would certainly like to see a 5 speed auto.