Yeah, try adjusting the eq in the aux mode and see if you can fix it a bit.
The Bose system and the iPod integration are hugely disappointing. Whoever designed their iPod integration deserves a boot to the mouth. Why not just replicate the way the iPod works? Apple isn't the 2nd largest company in the world cause they're doing it wrong.
Furthermore, it takes like 30 minutes to scan my iPod for data and it misses a bunch of the music.