No. Pelini's issues against Wisconsin and other running teams had next to nothing to do with too much speed and not enough size. In fact, I think he made a big mistake trying to be just like everyone else in the Big 10. To me the issues were:
1) A huge athletic downgrade. When we moved to the Big 10 all the talk was about how our defensive speed, and overall team athleticism, would be too much for the conference. But we immediately tried to matchup with the rest of the league. We went from a defense featuring Gomes, Haag and David on the middle line, to one with Compton, Whaley and Fisher. David was still there in 2011, when we won the division, but after that, not alot of athleticism, especially at LB.
2) Two gap and two high. We were determined to keep two safties high to prevent big plays. The only way to do that is to play two-gap up front. This asked alot of a front that wasn't very talented (especially after Crick's injury in 2011, until basically today) and teams like Wisconsin could consistently grind it out. By keeping two safties high, we also struggled big-time with the QB run game, as we are all painfully aware.
3) Complex defense asking too much of the safties. In Pelini's defense the safties were asked to fly up and support the run on sweeps and counters and to play over the top on pass plays. Teams like Wisconsin, we able to pair jet sweep and counter looks with double moves and go routes on the outside, putting our safties in no-man's land. Which led to poor angles and record numbers for backs like Bell and Gordon.