I prefer aftermarket headunits as it allows for much better customization of the sound. For example, my head unit has seperate leads for front, rear and sub. This allows me to have 3 seperate amps controlling my speakers. Also, I have full eq ability to fine tune the sound as well as bass/mid/treb/sub controls for the overall sound.
Not even to mention the problems about the onboard amplification of sound Minhi brought up.
Personally I just find it a better option to rip it all out and start from scratch. A bad comparison....but if you put in a new floor/cabinets/stove in your kitchen...would you leave the fridge just because it's still working?
R