I currently own both (going to hand my TJ down to my son).
I can honestly say that the JK is a better jeep overall, just as the TJ was an improvement over the YJ (I owned a YJ too).
The 4.0 is a torquer for sure and has been reliable. Once I re-geared my JK and used the flashpaq, my JK engine is a better performer than my TJ. My TJ seems slow now every time I drive it.
The JK is very mod friendly and has great street manners, even lifted with big tires. Even though the JK has more "computer stuff", it is just as easy to work on as my TJ. Except for the gears, I easily did all the mods myself. Jeep made the JK with future mods in mind (except for the sheet metal).
The TJ does have thicker sheet metal, but the JK frame is way beefier.
Factory axles, skids, steering, and suspension components are also built sturdier in the JK. The JK also moved the fuel tank to a better location and took care of the steering box issues that the TJ has. Even if you don't get a Rubi with lockers, the factory brake-lock-dif system works way better than open difs on the TJ.
The interior layout, comfort, and ergonomics are far better in the JK. I laugh when people say they hate the JK because "jeeps aren't supposed to be comfortable".
I especially like the Shorter sloping hood of the JK for visibility on the trail. When I wheel the TJ now, The lack of visibility over the hood is quite noticeable.
My JK top leaked when I first bought it, but so did my TJ. I got shitty service at the Chrysler dealer with my other Jeeps, and have expected nothing less with my new one. Its a jeep thing.
I love my TJ, but my JK is definately my go-to vehicle now.