Personally, I was able to empathise with the mc's experience of bullying despite the points you detailed, but I do understand that it would have been more impactful to have been shown some of the scenes rather than them being described in the abstract. That could have clarified his relationship with Aine while in school, because as is, it isn't entirely clear why he stuck with them. Simping just isn't a realistic reason. So yes, we are left wondering whether there was a good reason, or whether he is complaining over nothing.
I still personally like the scenes which delve into the detail of a character's backstory, revealing a lot about their personality and how it formed. Some games choose to trickle every character's story out over a long course of time (this is done very well in Harem Hotel). However, I like the way this game occasionally chooses to dole out large chunks at a time. Emma's chapter made the most of this, delivering a very moving and self-contained mini story, which wouldn't be the same if it was spread across multiple chapters. The developer has also decided to take a more measured pace with some characters, such as the pizza worker / runner (I forget her name), and these also clicked with me.
Nevertheless, I agree that the pacing isn't always perfect, and Jess' reveal is an example of this. I imagine pacing is very hard to get right given the serialised development cycle of these visual novels. Fifty Shades of Grey is an (extreme) example of how serialised writing can result in a meandering mess (in case you didn't know, it was originally written chapter-by-chapter as a Twilight fan fiction). I think My Bully does an admirable job of threading the needle.