I should explain: Yes, $3k is on the high side. But if you ditch the factory door speakers, you lose quite a bit of bass / bottom end. Getting anything to work properly with the factory door speakers is very difficult (external amps / crossovers, lots of tuning). Adding a power sub in the trunk helps the lower octaves but still leaves a gap in the midbass range in the front soundstage. To do it right, you need custom door panels (like Jehnert) with one or two good 6.5" midbass drivers per door. That alone can be $1k for quality stuff, most people do not have the skillz to fabricate their own doorboards. Quality amps, head unit, labor to install, etc adds up fast.
IMO, a powered head unit driving the dash & rear deck speakers alone, will sound worse than stock. I still think getting the Becker 1432 mod with auxiliary in, and retaining the stock amps & door/rear speakers, with (optional) Rainbows in the dash, is the best bang for the buck. This retains the ability to run the CD changer in the trunk if desired:
http://beckerautosound.com/1432-1991/aux_input.htm
For the record... I have two cars with full Jehnert systems and separate power amps, several cars with all stock speakers & head units, and one 1992 where the head unit was replaced with aftermarket plus power amp feeding the stock door speakers, Rainbows in the dash, etc. The 1992 car sounds the worst, as it doesn't have the impedance correction and equalization built in to the factory amps. MB and Bose did a pretty good job with the factory stuff, and it's easy to make it worse if you're not really careful. YMMV, etc.