Jeffrey's problem is NOT that he's a nerd
Disclaimer: This is towards a small percentage of the fandom. Most people already agree with this take to begin with.
Some people in the fandom like to argue that Jeffrey haters only hate to see an actual nerd. Jeffrey is NOT hated for his nerdy kind. In game as well as in the fandom and the game tells us that.
In the sex rehabilitation program route he mentions that he got sent there for jerking off in the gaming club and in the route in which Nicole tries to get into remedial class he says that the school has a manga club. There are canonacally other kids at school who share Jeffrey's interests. Yet he still doesn't have friends.
"But Nicole and everyone else bullies him for liking Manga." Nicole, Jecka and Emily are bullies that are mean towards anyone. Yeah, they might bully him for thinking that playing video games makes you an unfuckable loser but the other hundred of students at the school that just don't happen to have sprites are unlikely to have the same mindset.
Jeffrey is disliked for jerking off in his club meetings, telling everyone he just met about his kinks and generally not showing any interest in others. He never asks about other's favorite shows or hobbies. He just talks about anime and himself in hope that they will eat him up and put him on a pedestal for being so wise and misunderstood.
And honestly, that's what makes him one of the best written characters in my opinion because his mindset is so realistic. Two things can be true at once: Bullying sucks and is often times undeserved but you also can be to blame for how other people view you. What Nicole does to him is cruel Bit he could easily be friends with a person from the manga club if he just behaved normal. (He said himself that he doesn't read popular mangas but hentai. Everyone else in that club probably wants to talk about Attack on Titan and visual novels and Jeffrey just comes in and explains how cool incest mangas are and that RapeLay is the best game ever created.) I met a handful of people that are just straight up disgusting or cruel and then think that everyone hates them for being goth, watching anime or being gay. An ex friend of mine was like that. I dress alternatively sometimes, read some manga myself and am bi. At one point the reason why people keep leaving you is because your attitude sucks.