Personally I am not all that sold that the system you play in college has much to do with your success in the pros. Brady was far from a pro system in college but he sure has made it in the pros. I think that it's just a selling point for some coaches and George's comment is pretty accurate. I want my Gators to do what is best for the Gators and not what's best for the NFL. If Kelly is successful at Notre Dame, and I think he will be, I doubt Notre Dame fans will much care that his system may not be like the NFL.
Actually Brady did play in a Pro style system at Michigan, in the sense that the UM QB's under Lloyd Carr were always under center, and the RB were either in the I formation or a 1 back set and the used the 2WR and 1TE lineup like most pro teams.