You're a new defensive coordinator. Your new players may know your reputation, but they aren't familiar with your scheme on any intricate level. Fans think there was a lot of similarity between you and your predecessor, but in reality the reads, assignments and tendencies aren't exactly what your players are used to.
You spend the offseason working with your starters, teaching them where to be and when to be there. They're talented, they pick it up quickly.
Then, one by one, they get injured. They're replaced by backups: in this case not as much experience, in that case not as much talent, in all cases not who you spent most of your time with in the offseason. So there are more slow reactions, more blown assignments. But the injuries keep coming. Now you're scrambling. You're digging deep into the depth chart now; a few guys are having to play entirely out of position. They have even less talent and experience. You throw away most of your playbook - you're fortunate just to get all of these guys lined up right on any given play.
Do you see why this would lead to a struggle on defense? If he had been here for a few years already, I would hear your viewpoint. Then these deep bench players would be guys with system familiarity - maybe they aren't as talented as the guys ahead of them on the depth chart, but they've been around a few years and they generally know where to be. Shoop doesn't have that luxury. He's dealing with players with no experience, a deficit on talent and a lack of knowledge.
IMO expecting anything from the defense is unreasonable given the current circumstances. This year is an anomaly.