Notre Dame's formula for success had two key ingredients. First, Notre Dame didn't allow many explosive plays. Only South Carolina, Oregon, LSU and Alabama were better at preventing explosive plays against the run and pass, and only Oregon was better at limiting yards/completion. Second, the Domers allowed only 3.4 points/possession in the red zone. In other words, opponents were able to move the ball, but Notre Dame didn't allow them to score from near the end zone or far from it. Notre Dame also forced more turnovers than most.
The Notre Dame offense matched the defense's strengths with weakness - they struggled in the red zone and were far from explosive. They maintained long drives, ate up clock, and often reached the red zone, but from there they kicked a ton of field goals. Only a dozen teams scored fewer touchdowns per red zone possession. If they could have converted half of their red zone field goal attempts into touchdowns (which would still place them in the bottom half nationally in red zone points/possession), Notre Dame would have jumped from 59th to 25th in points per possession.
The Notre Dame offense left a lot of points on the field, but a lot of offensive talent will not be on the field in 2013. If we assume some regression in red zone defense, Notre Dame could fall back to borderline top 25 status in 2013. Then again, they could pull off a series of improbable wins and ride the luck of the Irish to another showdown with the SEC in January, but I'd say the former is more likely.