The Gen 3 system seemed VERY dated, while the Gen 4 system seems only somewhat dated.
I just liked the look of the Gen 4 better. I have a Gen 5 in my Prius and the Gen 4 is more reminiscent of that.
The sound quality of the Gen 4 seems vastly superior over the Gen 3 head unit. (IMO)
I found the answer to my own question about the CD changer. Apparently you need this adapter to plug in the old style CD changer plug to the new style.
Toyota part 08695-00370