As you say, a lot can be explained by a true freshman QB and Molk's absence. Not having a healthy Carlos Brown or Brandon Minor for most of the season hurt as well.
I also think we're going to find out that Forcier's shoulder injury, which he suffered in the Indiana game, was much worse than we were led to believe. During the OSU game, the announcers mentioned that he was getting treatment from the trainers between series.
Lastly, Michigan had one of the worst red zone offenses in the country. The Wolverines were probably the worst in the conference at leaving points on the field.