I would have to say that the main difference in my opinion between the two schools is the tradition and values that is instilled in boys upon arrival. Some of the traditions that are learned in St. Peter's are Jesuit traditions; that is the idea of brotherhood and emphasis on education- it is one of the very few schools that I know the boys will donate or attend alumni functions years later to show support. I liken the attitude and confidence the boys develop to the attitude and confidence of a Marine. Not to say that students from McNair lack esteem or pride, but it is not often (or hardly at all) that any of my friends or family who attended McNair visit the school 15yrs later
One other difference while obvious is still important none the less, is the religious element. That is not to say it is either good or bad, but religious based classes exists in one and not really the other.
I'm not entirely sure if I understand or agree with the idea that the kids are the difference, seeing that most of the kids can go to either school (except of course the girls).
Full disclosure... I would hope my son would choose St. Peter's