The top design was new for the JK. Lots of subtle differences between the TJ and the JK, some good and some not so good. I've got a pretty crappy top on the TJ that the Dealership I bought it from put on there to replace a worn out factory top. Other than some minor issues that were easily fixed, I haven't had any problems with the TJ leaking. Heck, I've got two gorilla tape patches on mine and it still doesn't leak enough to bother with. And it's a crappy Rampage top made out of saran wrap and monkey spit. The top itself on the JK is a really high quality piece, but the seal designs are horrible. I'm pretty sure that Bestop still makes the tops and Chrysler designed and builds the rest of the assembly. It's super quite, fits snugly without flapping around, the sun rider flip back thing is really cool and everything works the way it should. But it leaks, badly, on some of the JK's.
So now I'll be fiddling about with JKU instead of working on the TJ or heading out into the puckerbrush.
Oh, as an aside, the 3.6 is an amazing engine. The drive train on the JKU seems to be working out well so far. Good economy, lots of power and very smooth. The true test is when it cacks it's first hairball, and I dive in to fix it. If it is easy to trouble shoot and repair, then a leaky top won't seem so bad.
