One of the leftovers from the Kelly days at ND is a tendency to play at exactly the level of the competition. A lot of Fulmer's teams did this as well on The Hill. It's a hard habit to break.
Also, Kelly never really bothered to recruit qb talent and did an even worse job of developing the quarterbacks once they got on campus. Most were like current ND OC Tommy Rees. He knew what to do, he just lacked the tools and the training to get it done.