I've got an 06 stereo in my 05. It fits fine and uses the same harness. It's a 10 minute job. I'm not sure it was worth it though. I do like the volume knob and that it plays wma's, but I haven't found anyway to use the AuxIn. Plus, every now and again, it will just switch to the next song before the song ends. It might only happen once a week, but it is annoying. I read on some other threads that several 06 stereos do that. I'm sure Toyota will replace it under warranty... in your 06 Scion.
So I guess my advice would be stick with the 05 stereo or buy a nice aftermarket stereo.
So I guess my advice would be stick with the 05 stereo or buy a nice aftermarket stereo.