The stock system sounds ok, for a stock system. I've certainly heard worse.
More significant with the stock system is what you don't hear. Nothing below about 100 hz... or maybe 200 hz. Just no bass whatsoever. Similiarly high pitched sounds seem to be lost as well. The mid-range is fine, and for sports talk radio, it's dang near perfect. But for most music, you really are missing out on a lot of the sound that's should be heard.
I don't know if the speakers or the head unit is to blame. Probably a combination of both.
I'm currently undergoing a significant upgrade project to replace the entire system. Details can be found on my website noted below. Total cost for my system will probably be cost-prohibitive for most, but it will solve a number of "problems", not to mention increase the sound quality.