I give props to Al & Ed. I think their's is very cool and wild. I took a different approach. Here is what I posted in another thread in regards to my upgrades. At least one other person found it useful. IMHO it is the Ultimate Smart stereo because it gives amazing sound with no loss of space or useability. I can play this in a parking lot loud enough to entertain a large group of people.
Here is what I did to mine, just to give you ideas. The AVICD3 is a good choice because it give you nav, dvd, ipod, and a host of customization and other connections for under $1000. I had a custom faceplate made because I did not want to wait for shipping on one. This one matches, but I can repaint it or wrap it to customize it more.
I really like the Alpine PDX amps. Sound quality is great, they are digital and generate little heat, and are really small so they fit under the seats. I have one that is 4x150 and one that is 1x600 RMS. I thought about adding more power for the sub, but after it broke in a little, I'm not sure it is necessary. Sound quality is great. The new JL digital amps would be another great choice when they are available.

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I used C5 JL Audio 6.5" in the doors. As I mentioned, they only required a little bit of trimming on the door panel to fit. The door panels will still take the factory speakers back if I need to switch them back. I had the tweeters of this component set put in the factory tweeter location but I am considering moving them to the pillars. Any quality 6.5" should be a big improvement over the factory. I am not sure why a car audio place would tell you there isn't anything they can do for $600. You could easily get a small amp and decent speaker set installed for this price.
We installed the sub under the dash. I got that idea from this forum and highly recommend that option since there is cavernous space under there. Even with a JL 10W3 (a beefy sub), we lost no space in the car and can still easily get to the battery / fix a flat without removing anything.
We went one step further since we are using this as advertising and demo purposes. We used the second set of channels from the four channel amp and run a large pair of outdoor speakers off of them. We used this setup the other day at an event at a bar. We had more people standing outside by the car than inside the bar because they said the sound was better out there than inside. We got a kick out of that.

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Realistically we could hook up any other home speakers to this setup due to the way we designed it. We can also easily disconnect the rear / outdoor speakers if we need the room.
Don't let anyone fool you. This is without a doubt one of the easiest cars to work on and upgrade. With removeable door panels that anyone can take off and a battery that is located inside the vehicle, wiring and access is super simple. Even the carpet is designed to come up with no effort. If you have the upgraded sound system, you can literally reach up under the dash and replace the tweeters without removng a single panel or part of the dash. If you are looking for an upgrade path, start with replacing the speakers and adding an amp. Next go for a sub and amp. Finally a head unit will ultimately clean up the sound quality and add a ton of features. You can do it in stages if you want and it shouldn't cost you any more overall than doing it all at once.