Rich,
The Ducks led at halftime, and lost big to USC.
The Irish led with 2 minutes to go, and lost by 3.
The Irish have a stronger schedule based on Sagarin ratings than Oregon does.
Using your "stupid penalties" logic, if USC fumbles into the field of play instead of out of bounds, ND wins. If Bush doesn't assist on the TD, ND wins. If Quinn hits Schwapp on 3d down, ND wins. If Ambrose Wooden turns his head and arms around a split second earlier on 4th and 9 for USC, ND wins.
You needed things to break right to lose closely. A few similar breaks, and ND would have won.
No doubt the loss to Michigan State hurts the argument, the way they fell apart later in the year, but two losses by a total of six points counts for something, whereas, despite leading by 13 at halftime, Oregon lost by 32 to one opponent, a common one to ND, at home. The Stanford game, however, shouldn't hurt. You can't tell me Stanford was the same team Saturday as the one that lost to UC-Davis. It was playing for a bowl game, on a night that it brought out all its legends. It showed itself to be a very up and down team this year.
You can explain why you think Oregon deserves a BCS bowl, and you may be right. You can also explain why ND deserves one as well. At the times in which the games were played, it beat ranked Pittsburgh, Michigan and Purdue teams on the road at the beginning of the season. How they performed later cannot be separated from the losses ND put on them, because it Michigan's and Purdue's cases, a loss to ND often affects the rest of their seasons.
