It's a little thing called progress. The new models all have improvements over the older ones. The JK has a lot going for it, more HP then the 4.0 oh though not the torque. But it's not hard to modify them with a simple tuner. In fact one advantage is the tuners do more for the 3.6 then they ever did to the 4.0. Other then that better suspension, stronger axles, more comfort features, and more tire clearance out of the box. They made appeal to every day people will still giving off roaders things they wanted. And before any one says something about the weak stock bumpers ask yourself how many offroaders have their stock bumpers right now any way. No point in building something every is going to change any way.
Now everyone has their favorite for whatever reason, styling, first car, first jeep, or just fond memories but the truth is when you sit down and look at the facts and figures it adds up that every new model has been designed to out perform the last.
As for the JK's getting high centered it has more to due to the long wheel base on the 4 doors then the gas tank location. In fact it is better located then the others since it is mid-ship tucked up close to flat with the frame rails while the others hang it out the back and protect it with skids it still takes a pounding since it's what limits your departure angle. It's almost always the thing most wranglers hit when coming off of a ledge.