Ok, I've been working on ways to get the stock Bose system to sound better since I got my car. Two main reasons I wanted to try to work with stock:
1. Have no desire to rip this car apart. Have been heavy into car stereo since 2000, and frank I'm tired of it.
2. Cost: The Bose system actually does a great job of creating a stable center image. At a minimum the investment to get a similar stage would be $1500-2k by the time you factor in a processor, amplifier/s, speakers, sub. The JBL MS-8 is one that I've used before that does auto-tuning like that, and that alone is $500. Granted it does a lot of EQ'ing, T/A as well.
So, here's what I found gets it sounding the best so far:
1. Set HU Bass/Treble completely flat (0). Centerpoint and the other processing in the stock HU Off.
2. Use a music player that has a built in EQ. I'm currently using the stock music player on my Epic 4G Touch (Galaxy S2).
3. Cut 1k and 2k Hz at -5 or -6 dB. I have 1k cut at -5 and 2k cut at -6, but you can play with it to see what sounds better to you. Also do -1 dB at 200-250 Hz to take out some of the resonance in the mid.
What I've found is that the top end is pretty decent for stock speakers, and the bass is much, much more natural than using the built in bass boost. Reasonable impact for a stock system. Overall, the midrange in this setup is just too damn strong, and it actually hurts my ears. Now, I can crank it pretty decent and not cringe.
My $0.02...do with it as you wish.