I have owned about every kind of Jeep from the 41 Military to the new JK with everything from a 4cy to a V8.
What kind of Jeep you want depends entirely on how you (honestly) plan on using it.
I currently have a 2006 4cy with the manual and air and a cloth top and it is fine for running around on forest roads, some easy off road use and lite towing (1500lb).
I also flat tow it behind a motorhome to use in both urban (LA) and backcountry (Death Valley) use. I have driven it 75mph for hours and have had no trouble.
I have never owned one with a automatic but I think that would be a plus if most of your driving was stop and go city use.
I will add that I have seen Jeeps do some pretty serious off roading with a automatic and was very impressed with how they would handle very slow speeds on very rocking ground.
Whoops...my typical ready, fire, aim.... didn't realize you had bought one ...sorry about that...bart