I have to change the USB setting every time, too. (Galaxy S6 on Verizon, Hyundai Sonata.)
I've also noticed that Pandora starts up immediately. It's extremely annoying, because I have to back out to the Hyundai main menu, turn on the radio (or Sirius or CD or whatever), then go back into Android Auto.
Has anyone else noticed additional screens since the Marshmallow update? Now, when I press the button to exit to the Hyundai main menu, I get a splash screen that says "Are you sure you want to return to Hyundai?" (or something like that). I don't remember that before.
I've also noticed that notifications about texts seem to disappear faster and without a pop-up sound. They really need to streamline the whole approach to texts in AA.