I haven't touched this since before there was a Sandbox, and I've caught up from a new game in S1 to having just completed the S3 prologue. Aside from the general feeling is that MC is an idiot, it seems like a lot of story points about the family seem to have been dropped.
In S2's prologue Sam and MC have an entire conversation about Don and Olivia knowing about magic and how they should talk to the headmaster about it because it's a big deal. They never actually mention it to anyone in S2, and it's not addressed in the S3 prologue.
In S2 Ashley says she's been sexually harassed by Don and it's one of the major reasons she ran away, but in the S3 prologue she's more concerned with Don cheating on Olivia? Also Don wasn't actually cheating in S2, Irene's mom was just a super annoying nightmare customer. Yet in the S3 prologue he actually is? Also in S1's prologue Olivia and Don were the stereotypical nasty guardians (like from Harry Potter), but that's seem to have gone away entirely.
It makes no sense if you actually hit all these story beats in a short period of time like I did, where you actually remember clearly what happened.
Edit to add: Why are all the new freshmen 19, the same age as the sophomores?