I may be a little late on this, but what I found is that the system is heavy on synthetic bass and kick drum, but weak in the bass guitar range. There are graphs on this site that show a large dip in the area where the bass guitar operates. It's almost like the designers only listened to hip hop.
As a bass player who is also a basshead, this sucked. I also felt the system had a lack of clarity up front (but not from the back seat surprisingly, maybe they designed the car without seats installed)
I only like changing out what is needed, so I am doing my changes in steps and let it break in before changing the next item. I only changed out the front doors at first for the infinity kappa 693's, I had to pump the bass on the EQ to +9, but the entire 30-200 Hz became audible , clean, and smooth.
I could hear the kick as well as bass guitar. As the speakers broke in (took 3 months for me(!)), the low frequencies started getting louder and louder but still smooth and flat without any apparent frequency holes like the factory system has. I did lower the bass on the eq to +6.
I more recently changed the center speaker to the infinity 3022cfx, and the clarity improvements were astounding, I even bumped up the bass to +8 to keep it full sounding.
If I fade from front to rear, I can tell the rear doors are very midrangy, but together (fader centered) it blends well.
This is a good and cheap setup for a system improvement, only changing 3 speakers. I got everything on sale at Frys, it was $110 for the doors and $45 for the center, *huge* improvement, would do it again in a heartbeat even if I had to pay full retail. The speakers themselves seem to be a bit higher sensitivity, so the radio is also louder than stock. This would probably be enough for most people quite frankly, and it's fairly cheap.
My next item, being a bass head and all, is to upgrade the sub with infinity 1200S subwoofer in a custom box. My plan is to do just the sub first (yes I know it's a single VC but it is very efficient, so I'm just going to run one channel at first), see how it is, then if needed, take the unused channel and run it to a an infinity 1000s sub under one of the seats (the drivers seat seems to have the most room, and it looks like it would fit in a proper sized box). Because the sub channel gain on the factory amp isn't able to be adjusted, the infinity speakers will allow me to change the impedance from 2 to 4 ohms, which could be enough adjustment to flatten it should it be overbearing.
After that, the plan of attack for me is take a Audiocontrol lc6, sum the front tweeter, door and sub channels to an infinity class D amp, and drive the front doors with a full range signal (Factory is 60-800ish), and the sub(s) with a crossover around 60-80 Hz instead of the stupid 32ish Hz crossover the factory has it at. I am undecided if I am going to let the factory amp also drive the front tweeters, or power them off of the full range door amp; my understanding (though I haven't disassembled it yet), is that there are caps installed on the tweeters for high pass filtering in addition to the DSP digitally filtering the lows out. Easy enough to add if not.
I may also sell off my lc6i and infinity amp, and just run a single LC6.1200 or the like so I can completely tune the system, but I'm not there yet and it probably isn't needed unless time delays with the add on amp causes issues.
Here is one of the frequency response threads.
Factory Frequency Response - Page 2 - Jeep Garage - Jeep Forum