The RB1 (navigation) head unit seems to send a better audio signal than the AM/FM/CD/Tape unit. I noticed a dramatic improvement in audio quality in my TJ when I upgraded to an RB1. You should be able to find one pretty cheap these days with a bad disc reader. You won't have Nav or CD function with one that has a bad disc reader, but still get the improved audio output with your wired input/bluetooth device.
If you want to go with an aftermarket radio, you are limited to a 1DIN radio with a fit-kit for the WJ dash. Digital Media Receivers generally have all the functions you could want on a headunit with a reasonable price tag, they just don't have a CD player.