Hey everyone, I have this same problem. I noticed that the bass was extraordinarily heavy and my ears were killing me. I played around with the base and it was a no go. Then I turned off the Bose AudioPilot in the settings and it seems to have gone away. Sure, I hear more of the outside world, but for in town driving, that isn't bad. I will be trying it on the freeway this weekend, though.
I read a huge chunk of this thread and I was wondering if anyone tried this? The stereo isn't so bad. My biggest gripe is with Intellilink. It has a hard time handling Pandora and my iPod. I suspect it needs extra RAM or something.
Anyhow, I understand the mics are messed up, but is disabling AudioPilot not an easy workaround?