The Mach 1000 system in my 04 Mustang GT is pretty damn impressive for a factory system. 4 tweeters, 4 midrange, 2 woofers and subwoofers, each with thier own outboard amplifier with 6 disk in dash changer. Definatly one of the better Factory systems out there.
As far as factory systems go i havent heared one yet that compares, then again, i havent heared the systems in the high end (70k+) cars either.
My roomate has a 2004 Dodge Ram Hemi with the infinity sound system, which is pretty good but still not as good as the Mach 1000 system
Personally, im my view no factory system comes close in quality to a well done aftermarket system. Im not talking about just BOOM BOOM either, i mean clarity, detail, and the ability to hit any frequency with ease.
If you want high refined quality audio in your car, dont bother with any of the mid level factory systems (bose, shaker, mach, infinity, etc) instead go to a reputable car audio place and talk to the kids there and tell them what you want.
See if you can find a place with some Class-5 installers. These guys are usually just as knowledgeable about car systems as an audiophile is about home systems, and thier audio goals are not much different than an audiophiles. Im sure thier car's go boom, but i bet the detail and clarity they achieve would put ANY factory system to shame.
Most installers are serious about sound systems and would jump at an opportunity to work and install a true high end car audio system. Im sure they would love the challange and welcome the idea of working on system that is not one of the normal crunchy bass systems that 90% of thier install clients seek.