The basic system Pelini ran was a 4-3 (7 in the box) with one of those lb's being the Peso guy, who was a hybrid between run and pass and often acted as a 5th DB, and had to diagnose the play correctly each time, to put himself in the right position to make it work.
Tony is basically doing something similar, but in a 3-3-5, (6 in the box) so he needs one of the back 5 to assist in run support.. and I'm not certain if there is just one player who has this responsibility or if it is shared, or if there are even pre snap reads involved.
Against a team that can both run and pass, you have to try to shut down one of those options, and many times, coordinators like to shut down the pass, because a good passing team can score quickly on just a play or two.
This leads to the scenario where the running game eats you up and tires out your defense, and is what we saw against Illinois and what happened with Bo and Wisconsin too.
If you shut down the run game, they are going to have to throw, and you will get burned once or twice quickly, vs shutting down the pass and making the other team move the whole field and get first downs via the run. So intellectually it makes sense on paper, but in practice it doesn't always work out that way.