The quarterback wasn't the problem in 2008 and 2009. When you have a substandard offensive line in 2007 and 2008, along with a terrible defense was single-handedly responsible for costing us three close games in 2008, and all of our lost games in 2009, that pretty much tells you the whole story.
Both of those years (08 and 09) should have had BCS bowl appearances.
Jon Tenuta's "jailbreak blitz every down" allowed even mediocre offenses to pick us apart. He ended up being the second worst defensive coordinator at ND of all time. I'll let you guess who the worst one was... ;)