I am speaking from a more general sense I guess. JK is better on-road, as a DD and for long trips. JK is more capable off-road. JK is larger yet gets significantly better fuel econmy (in my experiance at least). JK can fit 35's with a budget boost.

As for specifics, some truth to that. Would I feel better if the JK sheet metal was thicker, yes. Practically speaking does it matter, no. The 5 speed is probably a bit stronger than the 6 speed, but I think they are going for fuel economy. Never had water issues with either the TJ or the JK, so can't speak to that. I do feel the passenger seat set-up for rear seat entry was much better on the TJ, but since I have rear seat passengers once or twice a year it's a non-factor.