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Not sure of the year you have but it could be from the analog cord your using. My 06 has terriable sound quality with the cord I'm using. It's a non ML system, I'm planning on using a better quality cord and see if that improves overall quality.
The cord should not matter. It's a digital transmission; one cord's 1's and 0's isn't magically better than another cord's 1's and 0's. It's probably the source material, or it's the way Bluetooth compresses audio.