I think Prot hit the trouble spots petty squarely.
But there are some perks to the JK compared to older models though - the Jeep my JK replaced was a '76 Cherokee, so that's where my opinions come from...
Highway manners: The JK actually has some. I live in Colorado, 30 minutes from what I figure is some of the best OHV land in the world, and the thought of driving my old Cherk up there some days was enough to make me not want to go. A half hour at 65 in it was enough to simply wear a person out.
The 'Rubi on the other hand is pretty much your average highway car, until you put it in 4-lo and hit the diff locks and swaybar unlock buttons... Then it turns into a mechanical mountain goat.
Gas mileage: The JK seriously trumps my old Jeep in this department - about 20 on the highway and 18 in town. The '76 got about 12 on the highway and 8 in town.
Technology: Yes, the JK has more computing power than your average third world country, but this has proven to be useful... I certainly wont miss having to ether the crap out of a big 4bbl in the dead of winter and hope there's enough juice in the battery to get fuel back into the bowls, or getting out to flip hubs, or having one tiny speaker in the dash that was trying to overcome 3" magnaflow'd exhaust, or any of the other stone-age stuff I was so used to. These aren't things you've probably had to do with your TJ, but for me it's a pretty nice change.
I think my favorite thing right now is that the 'Rubi tells me when it would like to have the oil changed and how much further I can go on the gas left in the tank... That's pretty neat.
Safety: The JK actually stops when you would like it to... With the '76, standing on the brake pedal was merely a suggestion to the vehicle that slowing down would be nice... And everything was well adjusted - 4-wheel drums are just, well, not very good.
Suspension: Lets face it, there's a reason the world moved away from leaf springs... The '76 was a harsh ride and to get any articulation out of it, you had to get pretty extreme with some welding gear. The 'Rubi just works, and works quite well, and you don't suffer from internal bleeding from washboards.
Drivetrain: My '76 was essentially a tractor - 4:88 gears, T18 4-speed with granny 1st, and a D20 transfer case with the terra low kit in it... Basically it was a three speed as 1st was useless for anything other than crawling and fourth would get you to 70 if you held on really tight and watched the pyros like a hawk...
The six speed in the 'Rubi is a godsend, really. Sure, you get to shift a whole lot due to the close ratios, but it's sooo nice to 'have a gear for that', no matter what you're doing.
But, overall - for me at least - the 'Rubi is still a "Jeep"; it has real axles, a frame, real four wheel drive, lockers... Even though it has a lot more creature comforts and more gizmos, I can see all of my 70's era Jeeps in there still...
So I bought one.