I would imagine that you could keep the rear seat in if you flipped it folded when you were using storage. If you wanted it down then maybe a copy of a Tuffy type of arrangement.
As for the JK I am so far really liking it, some say it's not a true Jeep because of the softer ride. I have found it to be capable as well as a bit easier on the old bones, I have a 3" Pro Comp on it and it's good. I have a 6 speed that makes it easier when pulling my Chaser, the LJ was an auto. Also the JK has ample room for storage, not as much as the LJ. With it's slightly longer wheelbase than the TJ 2 door it still has more room and less drag over obstacles. I also like the electric windows and of course when the doors are locked with the remote the tailgate also locks, nice feature. Jeep has still not done a darned thing with the tailgate not being able to be locked in the open position.