It wasn't a mistake, from what I saw. USA simply decided on moving up to FBS at a later time than the other three schools, and EA was too far along in development to put them in. Their fans got up in arms, and EA agreed to give them four-star treatment in '14 to make up for the perceived slight.
I'd rather they find a way to get everyone's fight song right myself, but it's not my game.
I like this idea, and wouldn't mind if they threw in a couple of defunct conferences we could turn on to spread teams out a little more. There's so much they could do with the custom conference system, but as of right now, they haven't.