I don't flat tow my Jeep but I can give you some input on other factors. I would suggest looking at a '97 or newer model. They went to a coil spring suspension in "97 and they are much nicer to drive than the older Jeeps. I have the 4.0L 6 cylinder and I can tell you that this motor is absolutely bullet proof. I have over 200K on mine and it still doesn't use a drop of oil between changes and I have never done anything to it other than change spark plugs. If you want to install oversize tires you will also want the 4.0. The biggest down side to the 4.0L is the mileage. It only get 15-17 mpg.
I have the manual trans and it is still going strong as well. I did have to replace the clutch at 180K.
I know lots of people flat tow the newer Jeeps, but I don't know if they have to make modifications to them.