If you live were there is a lot of snow (like me) get the 6 speed. It is full time four wheel drive. The automatic with part time four wheel drive is useless. You have to leave it in two wheel drive if the roads are dry but if you hit a patch of ice you won't have time to shift to four wheel drive. Hello ditch!
When i was in the market for the FJ, i was trilled tofind out it was avaible in a 6 speed manaul, since a manual tranny has always been my prefernace. I then found out it was only avaible in full time 4WD. I was really disapointed since i felt a full time 4WD was just a waste of gas as my FJ is used as my daily driver and i live in northern califorina, so i didn't feel the need for a full time 4WD in an SUV like the FJ. Then i drove the 6 speed....
... And that was the real deal breaker. It felt like i was driving a big rig with the long throughs, and i didn't care for the space between the pedals. Just didn't feel right to me. Bottom line is drive both, and determin what your needs/wants are from a vehicle.
As far as whitch is better off road, that question just can't be answered by anyone but yourself as it really just comes down to personal prefrenace. Some people will argue that this tranny is better cause of this,.. Or this one is better cause of that. Both have there advantages and dis-advantages. Iv'e wheeled with both, and for the FJ, i felt that the auto was a better choice... For me. Find out whitch is better for you.
Like some of the previous posters I'm a manual trannie guy, have been for 35+ years and never consider an AT when given an MT option. With that said, the AT in the FJ is superb, the gearing spot-on, the shifting quick & positive, well matched to the FJ's mission. I have this recommendation, if you're sure you can be happy with the AT get it, there is no downside. On the flip side the MT is a blast to drive; smooth shift action, good ratios, and NO problem to master in sticky off-road situations.
If finese fails I just stomp the gas and let the ATRAC hamsters figure out what to do.ATRAC is a lot less useful in the MT, unless you are a master at staying off the clutch.