I like the idea of replacing the speakers also but not if they will just be underperforming from the get-go
Generally speaking, the speakers are not the problem. The biggest problem with any stock stereo, no matter the automobile make/model, is the lack of quality power. Now, this lack of stock power can be corrected with the addition of an after market amplifier which more then likely will open up another can of worms. For example, once sufficient power is added into the system then the quality of the speaker enclosures becomes apparent.
In the case of the JK the speaker enclosures are horrible at best. They are made out of molded plastic that does a very poor job at handling resonance and vibrations. In a nutshell, once sufficient power is added into the system the stock enclosures resonant like a swarm of bees which most people mistakenly attribute to bad speakers. This inaccurate assessment cannot be farther from the truth.
Now, there is truth in the belief that speakers can and do affect the output of the audio spectrum. However, in the case of the JK the speakers are not the problem, it's the lack of power and the quality of the speaker enclosures. The stock enclosures can be improved by adding 2 or 3 layers of resonance dampening material like Dynamat extreme or Secondskin Audio Damplifier Pro. This material will help eliminate resonance and allow the speakers to operate more efficiently.
Some folks like to add some sort of poly fill inside the enclosure because they've heard that this procedure also helps improve the performance of the speakers. Although this is true it's only true to a degree. There have been several performance tests done by respected audiophiles not only in car applications but in home applications as well that have determined that the benefits of poly fill are minimal at best. These tests have also determined that the biggest gains in performance can be had by reducing or eliminating the resonance created by poor enclosure construction or materials. Regardless, adding some sort of poly fill or fiberglass inside the enclosure won't hurt or diminish the quality of audio output from the system. If you want to perform this mod then rest assured you won't be screwing anything else up.
Another culprit in poor audio output is incorrect equalizer adjustments. The first thing most people do when they get a new stereo is maximize the EQ which ultimately decreases the distortion ceiling of the system. In essence, with a maxed out EQ your music may start to distort around 60% of the head unit's volume rather then 75% volume of a properly EQed head unit. This distortion caused by poor EQ adjustments is then blamed upon the speakers which again, cannot be farther from the truth.
When I adjust my EQ I start out with the bass, mids and treble set to "0". Then, if the music sounds too bright I turn down the mids and treble. If the music sounds too warm I turn down the bass. By no means do I ever adjust the EQ into the positive as my values live in the negative side of the scale. As a result, I'm ensuring that I can increase the volume of my stereo without distortion; at least within reason. Here's how I see it, if modern stereos are designed to start producing distortion around 75% of their output then I want to ensure that I get all 75% of that clean music out of it. Why would I want to decrease the distortion value by maxing out my EQ settings?
Now, after making all of the above corrections to your stereo you might hear the result and say to yourself, "It's too soft, it needs to be louder!". If this is the case then the problem is not power, speakers or enclosures; the problem is there simply is not enough air being pushed by your system. What is "air"? Well, in a nutshell, when you place your hand in front of the speaker you will feel a rush of "air". This "air" is the frequency waves that our ears/brains translate into music. The more "air" a speaker moves the louder the music will be perceived. Having said this, it's easy to now understand why larger speakers are louder then smaller speakers; it's because the larger speakers push more "air".
In the case of the JK there are two tweets and four 6.5" mid woofers. It really won't matter how much power you feed the 6.5" mid woofers because physics dictates how much "air" that sized speaker can push; a 6.5" woofer CAN only sound like a 6.5" woofer, it will never sound like an 8" woofer because it doesn't have the same surface area as an 8" woofer. This is why just blindly throwing lots of power to a speaker doesn't always net the desired results we're after. The best course of action is to find out the recommended power ratings of the speaker and provide that amount power, any more then that and you're wasting your money.
Well, now you may ask how in the hell do you make your system louder? The answer is easy, add more speakers AND more amplifiers. By adding additional speakers you are exponentially increasing the amount of "air" that your system is pushing, thus, making it exponentially louder. By adding more amplifiers you are ensuring that each speaker is receiving quality power and operating in a distortion free setting.
Adding more speakers and amplifiers is a pretty simple thing to do in a home setting but unfortunately, it's very difficult to do in an automobile. This is why car audio guys spend thousands upon thousands of dollars chasing the Holy Grail of car audio only to be disappointed with every venture. The "Holy Grail" just doesn't exist because there are too many factors working against a pristine stereo in an automotive setting. The best we can do is recognize the limitations of car audio and create a system that reaches it's potential. Then, LEAVE IT ALONE! If you start chasing the "Holy Grail" you will never stop.
Good luck all.