The point is moot now, but another reason you might want to choose the flash drive over an mp3 player in the AUX port is that by using the AUX port, you still have to operate the mp3 player, and it must run on its own power. By using the flash drive as storage, you get to use the controls, power, and display of the in-dash deck. A much better option if you ask me.
Unless you weren’t asking about the AUX port at all and just weighing mp3 player vs flash drive (both in the usb port). Then, never mind.