This notion of Scott being stupid, or always having had bad grades.
When the reality is, that Scott’s grades were actually pretty good before he was bitten. One of the teachers in s1 even adds a note that those bad grades in s1 were way below his usual level.
Deaton actually makes it a point to mention that Scott is one of the most responsible kids he knows. Also keep in mind that he's working as a veterinary assistant. I'm sure that Deaton wouldn't allow Scott to do that job if he didn't believe in his intelligence.
Scott might not be a genius like Lydia, but when he isn’t distracted by just having his entire body altered in something he doesn’t completely understand, some outside force trying to get him to kill his friends and having his entire life turned over, or having his girlfriend’s father try and kill him, he’s actually pretty good at school, because unlike others, he does not mind putting in the work in order to improve.