Here are a few observations after owning many Jeep Tjs over the past 12 years now.
We will only list problems we have experienced first hand or helped other fix/repair, that way no hearsay.
1) A/C blower motor switch circuit is troublesome, they like to melt switches if you use the HVAC a lot. There are several inexpensive solutions to stop the problem.
2) The Dana model 35 rear axle, Inherently weak if put to the test or abused. axle-shafts tend to be the weak link followed by spider gear assembly. lots of debates to read about for the solution/fix/upgrade.
3) 2.4 or 2.5 four cylinder engines, think long and hard of how you are going to use the Jeep. Some folks are immediately disappointed with the available power with the 4 banger. Some folks love them. Just do your homework. Not many bolt on mods will give it any more power and they are prone for head gasket failures
4) Fuel mileage, lots of talk about that as well. Our beloved Brick-like Jeeps just do not get great fuel mileage period, Again not a lot you can do to increase it either especially when upgrading to bigger tires, bumpers or fenders.
5) Severe rot on frames, torque boxes, fenders, tailgates and windshield frames
6) No start or crank. ASD relays, Crank Position Sensors and or Camshaft Position Sensor are all culprits. Fuel pump failure and lastly a faulty ECU can cause these issues