For me the sound quality of the JBL system is tolerable, but not the best (I have the 8 speaker system with navigation). It has some bass, and since it's handled by a sub it's not too distorted like the mid-bass in a non-JBL 4runner audio system (those sound terrible). The highs are OK, but not the best. It sounds like either the frequency response is not flat, or there's still some distortion. I rode in a car with a Bose system a few times, and it was incredible (I'm aware that Bose isn't that highly regarded in the audiophile world).
I think the first step I'll take is making the interior quieter by adding some sound deadening and a sound barrier. Most of the noise reduction will come from a MLV barrier, plus closing off the door panels. It's a big project, somewhat expensive, and it will probably add 100lbs of weight. A cheap and equivalent way to get the same effect is to wear earplugs and turn up the volume since that also improves the signal to noise ratio, but I think it's illegal (and kind of weird) to drive with earplugs. Less noise in the cabin will make the audio sound better at reasonable volumes, and it should make for more a more comfortable, less fatiguing ride on road trips.
After that, it sounds like I need to replace the rest of the system entirely. In my last car I was able to just put in some good speakers since the HU put out a clean signal. It made a huge improvement (better than JBL except for lack of bass), and the total cost was under $100. It sounds like the JBL HU and amp work together, and the JBL amp probably isn't sending a clean signal to the speakers if it's diverting the bass to the subwoofer.
All I really need is a volume knob and an aux input, so I might leave the JBL boxes in place and just wire in an amp and new speakers. Then if I end up selling the 4runner I can take out the amp and hook up the old stuff to the new speakers and it will have the OEM appearance.
I don't even need all 8 speakers. In my last car I just had two coaxial speakers (medium woofer with a tweeter in the center) in the front doors, and it was fine as long as no cargo was blocking the passenger side speaker. The car had spots for tweeters (empty in the trim level I had), but they were aimed at the windshield, which apparently results in bad sound quality. I never got around to upgrading the rears, so I just set the fade 90% of the way to the front, and I hardly noticed the lack of sound behind me.
When our first was born 12 years ago we decided to have my wife stay home. I grew up with both my parents working and rarely saw them so-to-speak. I never wanted our kids to experience the same thing (though I do not hold any ill thoughts of them as they did give me a great childhood and loved us). I just wanted my wife and I to raise our kids. We home school our three. We don't do a lot of extracurricular activities and such, but we have a great little family 
. I just wish they had a method to their madness. Why deprive our 4runners of sub 60hz frequency? I just worked on a 2015 tundra with JBL and the factory sub played down to 30-35hz.
