The stock system is alright but lacks sizzel and thump. I did one minor upgrade once that really made it sound nice. I kept the factory speakers in there and then used a pair of ultra small Eclipse tweeters and mounted them right next to the stock tweeters in the doors. Only had to drill a 1/2" hole and they sat behind the factory grill (Gen2). Then I put an Infinity self powered sub in the passenger rear corner of the trunk. Now this is VERY important, you have to tap of the wires feeding the amp for the subs signal, not the amps output to the speakers. The JBL amp has some super funky EQ curves (thats why aftermarket speakers sound like chit with the stock amp) and makes the sub sound terriable. I forget what wires they are though.
Anyway since the bass on the deck could be turned way down and the Infinity had its own bass controll the system sounded sweet! Nice crisp highs and deep bass.
That being said a $100 Pioneer deck, some $100 Infinity 6x8 Kappa components, $45 Refrence coaxials for the rear and the most sub/amp you can afford will sound 100x better.