These timeskips make it seem like nothing ever happened other than the MC's incidents and their aftermath. There was no quiet moment to talk things over, or forget about it once other stuff happens, really?
Yup. Even after they admit they were in the wrong, then form a pity group, they never once do anything other than sit around talking about how bad they feel. Nobody ever apologizes to him, even once, or tries to make amends, or anything. Step-mom hears things about MC and literally doesn't care if it's true or not (Chapter 6, Page 1). The girls do their thing, then decide not to talk to him because of Japanese reasons, and MC just... kind of... forgives them... for no reason. Everyone else decided he was the bad guy, then decided to ostracize him.
Only the step family did anything that might begin to put them on a path to redemption, but finally realizing he doesn't want anything to do with them after years of abuse isn't exactly going to absolve them in one go. But frankly, I don't even know where the hell this sudden change of heart came from in the first place.
Now she cares about him?
You could say the same about the girls. What could they do when things happened so fast? MC could say that he was running to get the bandaids, or that there's stuff falling in an earthquake. He used to be a jokester, so it's not like he was too awkward around other people to speak up.
Sure, maybe. Especially Shizuka. But the "victims" had all the power in the world to, at any point in the several years afterwards, to take it, any of it, back. They could tell everyone the truth. They could tell
anyone the truth. Hell, they could apologize to him in private. None of that happened, and it continues not to happen. They just decided to pop back into his life like nothing and mope around when he keeps them at arm's length.
The big issue here is you assume anyone would care what a boy says when he's been painted as the aggressor by a crying girl, but we both know that crying girl beats alleged aggressor any day of the week, and twice on Sunday.