Couple of observations, and then a question:
I just added a powered subwoofer to my base non-Sony 4-speaker system, and it makes a world of difference. After a few hours of playing with the stock system, my sound guy and I found it best to set the MP3 (iPod, in my case) to a flat EQ band, and roughly shape the sound with one of the preset EQ settings in the car system. Then, you can tweak the treble, mid and bass settings to flavour. Those of you who play guitar know that EQ is best set at the end of the sound chain.
Strangely, the "Rock" preset sounds muddy and awful, but the "Pop" setting is much better. My current setting has the treble at the mid-point, middle at -3, and bass at -4 (subwoofer has a remote control for deep bass and thump). The stock speakers work much better when not asked to handle deep bass, and provide a clean bass kick when they're not overtaxed.
Here's the question part: is it my imagination, or does the SCV level (supposed to control volume based on vehicle speed) actually act as a pre-amp? For instance, if the SCV is set to off, the sound system sounds ho-hum, even sitting with the engine off. If I boost the SCV to between 4 and 7, there's more sound energy everywhere. In other words, I'm not hearing a simple boost in volume...it's more like a pre-amp boost before the stereo's EQ. Try it...it's like the sound gets punchier, not significantly louder. I have the SCV set to 5, if that's helpful to anyone.