To each their own, but I have done installs from components, head unit, amp, and sub in my first XJ, up to fully integrated with OEM dash and factory amp in my BMW (holy expensive pain in the rear), to replacing absolutely everything involved in several other cars (down to gutting the car for the install). The single biggest factor is absolutely not the components or money spent, but rather the install and listening environment, and how well you can tune the system. And that is where the JK falls very short. It needs some CLD damping, a good isolation layer, and a good barrier layer to even start with sound quality. Beyond this, the entire vehicle is a hard surface that will cause reflections, it has a large amount of wind noise (not related to any of the things you can actually correct), the roof is close to impossible to help and keep functional, and a soft top leaves you no way for improvements. You will notice improvements more in a JK than you might in a nice car, but it takes a lot of work, weight, and diminishing retuns to get it to sound good, IMO.
Have you ever heard a ski/wakeboard boat with a "$5k" stereo upgrade? Ever notice that it is loud, and sometimes clear, but rarely actually sounds good, and it gets annoying to listen to pretty fast if you are just chilling on the boat? It is not hard to get better sound with $500 worth of gear in a bedroom, and be louder, more clear, and a better listening experience without ear fatigue. Just the nature of the environment. If you roll with the top down, then getting some volume and clarity are the difference in having music, or hearing some jumbled crap in the back ground, but do not mistake louder for better, in all situations.
You would probably see some gains with better speakers, an amp, maybe an upgraded sub (but the enclosure is a weak point as well). I dont know if I would do much more than that, for both security, and improvements could be lacking vs dollars spent, unless you are a top on, windows up, kind of driver.
Also note, I am a big fan of integrated designs and hate having a big sub box taking away the usefulness of a vehicle, or seeing other components. Hidden = well installed, for me, and that is usually a bit more expensive.
I wish I had all the money I have spent on audio gear over the last 12 years or so... But it did make commutes and trips a heck of a lot better.
As with everything, value is subjective to your needs, and YMMV.