I think it has more to do with Bo is afraid to sit anyone. Look at 2010 When Martinez got hurt. We had a capable back up in Lee and rather than sitting Martinez for the rest of year(or let him heal) and letting Lee play he risked further injury to Martinez than to sit him and happened again in the Wyoming game. Hell all we had to do in the Wyoming game was run the ball on their defense and we win comfortably. He doesn't seem too concerned about the health of his players.
I'm not so sure. David Santos lost his blackshirt and barely played against USM, if I'm not mistaken. And though we never found out specifics, the general consensus about Lee was that he was physically incapable of being the starter we needed him to be because of injury.
Whether fair or not, compare Pelini to the greatest coaches of the last 10 years - Pete Carroll and Nick Saban. There are some obvious discrepancies, most important of all the talent Carroll/Saban had and the proven (and alleged) NCAA infractions. But, those teams project sheer discipline game in and game out. They also show an ability to learn from mistakes and make in game adjustments.
I know it's not the most fair comparison for various reasons, but it's only natural to look at what the best teams have and figure out what we need to do to get there. All things constant, we lack discipline at crucial times, but I think that just comes with coaching experience and your ability to create/hire a good staff.