At first I did not like the sound coming from the system either but after going to Myer Emco and Crutcthfield for a replacement system cost estimate, I decided against it.
The head unit Honda uses is made by Alpine, of course that doesn't mean much since it is made for Honda so none of the Alpine kits will work directly with it.
I decided on installing the BASS kit. The sound is now comparable to a low end Acura system.
I knew going into the Civic it wasn't a premium based car and I didn't expect the audio to be mind blowing. As with previous comments, the speaker placement is questionable and most likely the reason why the system doesn't sound better than it should.
If you want to see how the BASS kit is installed, I did a complete write up on it on my website
http://www.abittans.com