You'll definitely get a better sound if you change out the speakers for after market ones. However I would not recommend running an after market sub on the stock amp (assuming it has a stock amp). When I had my 03 Tiburon I ended up disconnecting the stock sub from the stock amp so all the other speakers still worked (they ran through the amp too) and bought an aftermarket amp for my subs I put in the trunk.
Getting a better amp for the stock speakers might net you a little better sound quality but stock speakers are stock speakers.
I like the way it sounds. My dealer had an optional 350W EX and from the little time I drove the Civic it sounded really good (had my girl in the car, not the sales rep so I played my own CD). Honestly, if you want you could change the speakers but unless you're an audiophile (like me ), this will be sufficient.