I replaced just my headunit for a more modern one that has Bluetooth and HD Radio. Pioneer DEH-X7800BHS. It's not all a win/win, as these new headunits really need a constant +12V supply to keep the setup and audio settings which I'm working on next.
http://www.airforums.com/forums/f450...2v-174467.html
Sound quality is satisfying at this point with the stock speakers, because it's easier to access high quality sources (from the connectivity advantages listed above, as I don't use CD's anymore) and I spent more time tailoring the sound profile (add loudness and a bit more bass).
On the sub, you may also want to make sure the crossover is almost all the way so that it's not artificially filtering out bass inputs.