I own one of each.
- I drive a 2008 JKU X. 3.6L (or 3.8 I forget) V6, 4-speed Auto, 3.73 diffs. 2" spacer lift. 35" mud tires on 17' wheels, no front sway bar.
- my 18 YO son drives a 2003 TJ Rubicon. 4.0L I6, 3-speed auto, 3.73 diffs. 31" mud tires on 16" wheels.
The TJ has a much better engine than the early JK. Someone else called it gutless, that's a good description. To be clear it is fine on the hills and trails where we offroad but it's weak around town. The automatic trans in the JK, at least the early one, has a problem with the torque converter than Jeep hasn't been inclined to fix. Mine didn't show itself until 135K miles or so but I've read stories about folks having problems damn near from day one way back in 2008. I have a friend who owns a trans shop and he simply says the TC in this transmission (slang for transmission is also slang for a person getting a sex change and that's filtered!) is a POS.
I've told my wife on a few occasions that I could see me selling my JKU and buying a TJ. My son's Jeep rides rough but it has significantly more power than mine does. Both leak oil, it's a Jeep after all. We've only owned the TJ for about 20K of it's 173K miles but the JK has been reliable at now 150K as we're the only owners.
If you have specific questions let me know. The JKU was my first Jeep and I love it. The power is annoying but given the configuration and the fact that I rarely run with doors it's really an around town vehicle and a weekend toy at this point. I work from home so when it rains I generally just drive my wife to work and use her car. Obviously not everyone can do that.