I rant this every year. ND should be recruiting the same quality of horses on the OL as Wisconsin. And then using a smash mouth running attack as a first order tactic. Offensive Linemen love to get a groove going and pound the ball down field. Not Kelly though. It's not that he abandons the run too soon, it's that he never relies on it at all.
Doug Flutie made good comments about how effective running to the side overloaded with 2 tight ends was for ND. Right. Why not run that scheme out of the box to set up the passing game?
Lastly... I also always mention Robert Hughes as a key indicator Kelly's myopia. That guy was a really tough inside runner. So of course Kelly gave him minimum touches. And nothing has changed since then.