Here's something to think about:
During the season, our 1st team defense usually goes "live" versus our scout team. That is, our 1st (and 2nd team actually) will practice against our opponent's offense using scout teamers and 3rd teamers replicating the other team's offense. For most programs, it isn't a problem because their offensive personnel is the same as 90% of the personnel around college. Pro style or spread style QBs, RBs, OLs...etc. are replicating another team's offense. So really, they're just trying adjust to the other teams offensive schemes and concepts. We have 2 problems in this case: We have to adjust not only to another teams schemes and concepts, we also have to adjust to another teams personnel.
Think about it like this, and let's use Michigan State as the example. When Kirk Cousins (and NFL level QB) was at Michigan State, they could practice with a guy like Connor Cook (a future NFL QB) running the scout team offense against their defense. Cook was giving Michigan States' defense looks against a high level QB. Quality of players the defense has to practice against is a lot higher...therefore, the defense was getting tested a lot more, which in turn helps them during game days.
Now think about the personnel we have to use on our scout team. We have spread option (or triple option) personnel trying to replicate Pro and Spread style offenses. Last season for instance, we had a guy like Christian Campbell/Brady Swilling/Chase Martenson trying to replicate the skill level on offense of Clemson, UNC, Duke, etc. Those are not bad players, per se, but their strengths as players are better suited for GT's offense not the teams on our schedule, which means the look they can give our defense is not as good as say the personnel on other teams because other teams have similar personnel. That's just not at QB, but at other positions as well. Obviously guys on scout team/3rd team aren't as good as what defenses will see on Saturdays at any school, but when you get personnel that is similar to most teams, there's less of a gap to adjust to.
Maybe a reason why we see our defense do a lot better in the 2nd half than they do in the first half? Maybe because of the personnel we have to use during the week can't replicate looks that most other schools are able to do.
It isn't 100% of the reason why we aren't as good on defense as we should be, but it could play a part.