I just got my 13 jku with upgraded alpine system. In a nutshell, the sound quality is poor to bad. (background disclosure: I'm a bit of an audiophile, sold high end equipment out of college, have owned everything from Thiel speakers to Mark Levinson).
The sound is dull and lifeless. I did the polyfill and it helped a bit (bass got tighter). Boosted the treble setting to +9, this helped, but not enough. I finally dropped the bass to -5 and the midrange to -5 and got significantly cleaner sound. The overall balance of the sound was dramatically improved. The Bass remains substantial because the midrange is brought down to its level allowing the treble to scale higher relative to the rest of the music.
The radio and cd now have an acceptable sound (fair to good) for a vehicle. Give this a try.