The difference in the quality is the input type. usb vs. aux. just like radio quality is not as great as cd.
What options are available on the radio?
Actually you should leave the MP3 flat and change the EQ on the radio. That way you can use the same settings for your other items such as cd/radio. If you still notice poor sound then change the settings on the MP3.
Qualifications: installing car audio for 4 plus years.- MECP certified