I do hope for RNGeusEX attach this time as much as possible to whatever he had planned as story, if you want reasons for Sakuya to be in love with a loser as MC could be, we can argue that they known each other since kids, and mc was nice to her on occasions on a time when no one care of her in the school because she was a loli with boobies, too tall with a baby face with a hairstyle of which kids makes fun of her, so he came to defend her and that did an impact to her, stalking him since then, making her an insane obsession Hinata Style but with tints of School Days, or if you want, inspired from Yuno Gasai from Mirai Nikki...
Whatever their story is, mc could not be a bullied boy all his life, that must had beginning at some point in the past, more probably after Sakuya meet him, so, she never had a reason truly to help him against the bullies because she must known that he can defend himself, she help him against Netoru not only because it was affecting him but it was messing against her chance of a bond relationship with him in the time during work.
Whichever the reason RNGeusEX had planned for her, it could go in the past of MC, perhaps he had more mental issues, as being raised by his father, it could had been something related during the time he lived as a family with his both parents, perhaps his mother died or did an NTR to his father and leave them (sorry RNGeusEX I know you don't want NTR in this game but i was thinking in reasons for a kid to develop some kind of guilt because one of his parents disappearance meanwhile the another grew in lack of taking care of the kid until abandon him, but i still feel you must complete the circle about the mistery of MC's mother).
