The only problem I had was an axle leak at 35000 miles, but was fixed under warranty.
The driver seat started to wear badly at 80000 miles, which is reasonable.
The major thing that I was bothered about was the fading of the fender flares. I tried the polish thing still won't do it, so had to replace them
cost=$420.
The car is good if you do not go on long trips. It is so much fun with the top down, because with the soft top it is kind of noisy.
It is definitely not a fast car, but can handle good off road.
I own a 97 Jeep Wrangler SE also and have the same problem with fading of the fender flares. I buy the polish for tires and rubber to temporarily 'dye' them black again. I also have had problems with a oxygen sensor which would make it 'buck'. The Catalytic converter was replaced (under warranty) and the sway bars were just replaced (54,000 miles). I just got the brakes replaced... they would lock up when it rained. The plastic windows that zip up go off track if you aren't careful how you zip them. With all this in mind, I love it in the winter (not the warmest) in the snow and in the summer its great with the top down (don't get caught in a downpour).