I went off the deep end (to some) to fix it, but maybe you can take some of my solutions and just tone them down some. In addition to the build log (which I keep a link of in my signature to help), I also have some threads in the audio section with EQ and distortion graphs, so you can see what my calibrated mic was able to hear, like our ears hear (with averages where it counts, to account for a pair of ears and multiple seating positions.) From them you'll probably pick up that at first listen or so, it is tolerable but the more you dig into it, the more you realize it is fundamentally flawed in too many ways to be salvageable. Yes, you can just replace speakers or add amps, but there's issues that will be amplified (literally in ways) when you do this.
The hardest part of my fix is the MS-8 processor, which is discontinued. It is the ONLY processor (except the H800 Alpine) that properly handles center channel action. And that's a big deal, because with a proper center channel, the whole front Durango stage is very anchored/stable, and sounds fantastic.
Speaker-wise, you can definitely drop down some notches and still be happy. I went high-end (as high-end as 6x9's allow, specifically) but there's room to cut and get creative. Not ideal to do that but possible. Perhaps running an Alpine R 6x9 coaxial and then maybe the SPX PRO (replica) tweeters like I put in the pillars, with a processor and amp channels to control it would be a good compromise. Amps can be very small these days, so the fact we need a bunch of channels (at least in my build's case) is handled with many small amps that can hide away. You should be able to fit a single flat 10 in the trunk area by replacing the factory subwoofer area completely. It is possible to hide everything completely as well, but expect some fab time and energy there. But to this moment, I've got:
4 amps, 2 Sundown 10's, and my MS-8 processor all in that trunk area, and except for my processor which is mounted in the cubby hole area on the left rear, all the rest is fully under the factory floor panel so it is invisible. Full function of my trunk area is available, and it works. I wish I had a fast-and-easy cure for folks wishing to better the bass response in these trucks, but truthfully aside from polishing the turd that is the factory sub enclosure and/or sub, you just have to get crafty in the trunk area, and not be afraid to pull some panels to make it happen. I tried to document my process as much as I could in my build, to be of use. It was helpful to me along the way to keep track of it all, so it works out for me too.