I have the 2011 JKU and the stock sound was just awful. From what I have read the stock head unit purposefully underpowers your rear speakers. I replaced the stock head unit with a DNX7160, I'm sure there are better/cheaper units out there. I then had Alpine R-Types installed and the speakers filled with polyfill. This made a huge difference, but my system is still really underpowered and my amp is going in this week. I think one of the biggest changes was the polyfill in the sound bar.
I really wish I had just done these upgrades myself, but the dealership went on and on about me voiding my warranty if I screwed it up. Well, I went to a local business who screwed up various aspects and cost a good deal of cash. These upgrades are easy enough so that anyone with a few friends can complete them on their own. Just my $ .02