I didn't read all 9 pages to get here, so please forgive me if I am duplicating, but I bought a brand new JK in 2010. It was a v6 duh with a 6 speed manual trans and factory 3.73 gears. I used it to tow my street bikes to the track on a super light weight Kendon trailer, but the problem I had was at 45 miles an hour if I hit the clutch the RPM's didn't go down immediately, so if I was shifting from 3d to 4rth at that speed the trans would grind. The problem was if I waited the 3 seconds it took for the RPM's to go down, It would be way to slow for 4rth gear. This wasn't normally a problem unless I was towing really, but I was doing that every weekend.
I took it to the dealer multiple times to see if they could change the fuel map or do something for me, but they all agreed that it was a problem, but wouldn't do anything for me. I asked the aftermarket chip companies if they could build a fuel map for me, and they said that I wasn't enough audience for them to R&D it. So I decided that it was way underpowered and sold it.
Honestly I liked the JK other than that. I really believe it is underpowered, and mine was a 2 door, I am not sure what they are doing with the 4 doors, but now I drive a 98 Tj with a 4.0 5sp and 3.73, and it has way more power. and the fuel map is much better.
So to break it all down I like that there are more possibilities with the TJ, and it seems like it is a lot lighter and definitely has a better fuel map; that said maybe the JK does better for the emissions (I don't know) but it is a deal breaker for me.
Underpowered and bad fuel map with less options to change.
Now that said this was 2010, Maybe now in 2017 things have changed, but I don't really care because I am perfectly happy with my 98 TJ.
That is my .02