The JBL 10-speaker stereo is only $360 at invoice pricing... $450 at sticker.
It's worth it IMO, unless you want to rip it all out and put in something custom of course.
I used to be really into car stereo systems (had over 7 grand in a SQ setup in my truck, and that was at internet prices)... so I think I've got a pretty good ear for things and can safely say that if you got the base stereo and spent $360 in upgrades on it you would still not be able to come close to matching the overall improvement you get from the JBL stereo. True for $360 you could get a cheap sub/amp combo and definitely have more bass... but to get the improved clarity, imaging, high, and mid-bass/range frequencies is going to be quite a bit more extensive and costly because that's when you start replacing stuff rather than just adding on.
I also like the JBL setup because it has a center channel which will make it very easy to, in the next year or two when SACD/DVD-A and multi-channel satellite radio becomes a little more prevelant, get a true surround sound output instead of just surround sound downmixed to stereo.