I hear you

I guess we're in sync, but I'm going to start in the other end. Soundproofing at first, fitting new speakers second, fitting an amp third, getting a subwoofer (and amp) fourth. Then, if I'm not satisfied, I will check if I can test a JL Cleansweep or an equalizer somewhere (to see if it's worth the trouble, no idea what it costs...). And only then will I consider changing the main unit. But I'm expecting I won't even consider it.
But if you want to start on the other end, by all means do so. Fitting a head unit in the center storage compartment would be the easiest, I suspect. And if you put some trouble into it, I guess you could even mount it so that you can close the lid if you should want to (cheap theft insurance). By far the easiest would be to make a fiberglass enclosure that fits into the hole (with the lid removed), and just drill holes for the cables in the rear. That way, when you sell the car and remove the sound system, you need only refit the lid, and everything is close to original.