They cannot run the ball when they have to because of the Kelly Offensive scheme. No lead blocker (where is Anthony Johnson when you need him) and the delayed handoff does not lend itself running into 8 and 9 man fronts when the opposition knows you want to. The Irish have had the lead and the ball in the closing minutes of two or their last three losses and were unable to sustain drives and run out the clock. If we had a power running game both of those would have been wins. An offense that is not able to impose it's will in the closing minutes of games is not a championship offense.
Yes, the defense has real problems. The loss of Jaylon Smith, Mathias Farley and Sheldon Day hurts and they have not been adequately replaced but the lack of a power running game is at least as big a problem