I love stats as much as anyone. But stats can be presented in a number of ways to mean different things. Looking at ND overall, I come away impressed by their defense and how hard they play. Those guys are tenacious and they really play together.
Sure, they may win ugly, but still they win. I gotta respect that. ND is the kind of team that will make you pay for dumb mistakes and turnovers. If we don't turn it over and avoid penalties I like our chances a lot. I don't think they can stop our run game for an entire four quarters. But I also think their QB will be a headache at times with his scrambling ability.
I don't think anyone's really saying that they aren't a great team - certainly not me. Any team that makes it to the BCSCG - and undefeated especially - is, at the very least, a very good team.
It's just that they may not be as good as a lot of people - seemingly most of their fans - believe them to be.
As you said, stats can be deceiving. That's kind of my whole point with the differential analysis stuff, especially situational and targeted differentials. Sure, team A may score 43.2 points per game while team B scores 35.7 points per game. That doesn't necessarily mean that team A has a better overall, or even better scoring, offense - especially if the defenses that team A played averaged giving up 39.7 points per game while the defenses that team B faced averaged giving up 27.2 points per game.
The most important thing to do when looking at stats, and trying to compare two different teams by using them, is to use as many common denominators as possible. In some cases, such as comparing an SEC West team to an SEC East, that can be fairly easy and fairly accurate. Of course, you still have to take into account various unknown or unaccountable factors such as when the teams face(d) each other, playing styles, injuries, coaching adjustments, individual match-ups, and emotion just to name a few.
Those are things that a statistical analysis cannot really account for, making any statistical analysis flawed from the outset.
That doesn't mean, though, that you can't learn anything from them.