Hi guys. I have been watching and reading various forums for weeks and wanted to share my results based on a particular thread in another "wrangler forum." My JKU has the Alpine "premium" system with sub, hardtop, but currently with a Trektop NX soft top on, with the 130S head unit. This is a 2014 Sport manufactured in Jan 2014. I'm always on the lookout for making things as best they can be, but on a very strict budget. I decided to stay with the head unit based on others experience with these upgrades. I also left the front speakers stock, but modded the tweeters per below.

I upgraded my sound bar speakers to Polk Audio DB651 (http://www.amazon.com/gp/product/B000P0PF9G/ref=oh_aui_detailpage_o07_s01?ie=UTF8&psc=1), and stuffed it with polyfill. This update was a huge improvement in quality of sound filling in the highs from the rear.
Next, I replaced the capacitors on the stock tweeters. I bought a set of 6.8 farad (http://www.amazon.com/gp/product/B0002KR5ZG/ref=oh_aui_detailpage_o05_s00?ie=UTF8&psc=1). This mod was just as huge for me in the quality of sound out of the front! It really brought out the voices in music.
I replaced the sub with the Pioneer TS-SW2002D2 speaker (http://www.amazon.com/gp/product/B00K98535A/ref=oh_aui_detailpage_o06_s00?ie=UTF8&psc=1) and stuffed(loosely) the box with Polyfill. Overall, there was less bass, but agree this mod was for better quality bass. I left this sub as is and messed with the Treble, Bass and mid on the head unit, and at volume, it sounds great, but you don't get the boom that some people enjoy, and I wanted to have that on occasion. I would say that music is accurately reproduced as is though. The music source is a huge factor in how it sounds as well. I mostly listen to radio, and high-quality MP3's. Satellite radio just sucks!
EDIT:
After a few weeks, I finally pulled the trigger on an amp for the Sub. http://www.amazon.com/gp/product/B00CMC5022/ref=oh_aui_detailpage_o01_s00?ie=UTF8&psc=1 Precision Power i350.2 PPI iON Series 350 Watts Class D 2-Channel Amplifier. This thing is compact and combined with the Pioneer sub, ratings say this is a great match. I mounted it under the back of the rear seat on the passenger side, and just spliced into the existing speaker wires running into Sub, and attached the them to the High level inputs on the amp, and then ran stereo out to the sub. I set the amp to Low pass, and turned the low gain up halfway, and the high pass just to the first mark. I am trying to find a good accessible location to mount the remote for the amp, but being able to adjust the gain to the sub is huge! I am very impressed with the punch and boom the sub is capable of producing considering it being an 8" and in such a smallish box.

Dont forget to pick up a couple of these. http://www.amazon.com/gp/product/B0007WTEVM/ref=oh_aui_detailpage_o02_s00?ie=UTF8&psc=1You'll need a pair for the sub, and each set of speakers you replace.

Overall, being a Jeep and not the best vehicle for a sound system to begin with, I am amazed with these mods and will most likely never touch my sound system again. Total spent, less than $300.