I posted in another thread that I think, sometimes, an injury bug really can hammer a team no matter how physical or how good your strength and conditioning program is. I also said in that thread I believe it's been awhile since Nebraska looked like the more physical team on any given Saturday. I think this has more to do with the style of play, though. If you compare Stanford and Nebraska, for example, Stanford just physically drains and wears opponents down. But, they also run a very powerful and physical type of offense quite different from ours.
The big thing to keep in mind here is talent as well, imho. The talent discrepancy between 2009, and now, for example, is pretty substantial. Most notably on the defensive side of the ball. I think the group of young guys we have on that side of the ball have a ton of potential - don't get me wrong - but 2009 had fairly veteran/talented defenders where we were rocking a lot of young/talented defenders this year.