I use the auxiliary jack for my satellite radio and it sounds great! On my first gen xb I just used the fm out to play the satellite over the radio and the sound quality was adequate at best. but with the new 2 gen xb I like having it wired right into the sound system and it is much better. The satellite and i-pod both sound really great. Kudos to scion for the improved sound system. Yes you can use a male / male cable to wire your non-i pod mp3 player. When I test drove my scion I wired my i-pod in that way to check the sound system "was not aware the ipod cable was in the glove box" I played Powerman 5000 "When Worlds Collide" and it sounded good ha ha. So I think your mp3 will sound good with the auxiliary jack. Another good tune for doing a sound check is "Nonpoint" (Bullet With A Name On It.) Good luck with your new scion when you get it.
The car comes with the male-to-male cable necessary for hooking up ANY audio device with a 1/8 inch audio-out jack to the AUX port. It can be any MP3 player (including iPod) or even a laptop, as long as the audio-out jack on the device is the 1/8 inch jack. Headphone jacks are normally this size.
Also, it should come with the iPod adapter cable. Mine did, although I will probably never use it.