Alot of novels have either very handsome/pretty mains or suuuuper average im looking for a protag that makes people want to look away or outright run from his/her hideous appearance. NO YAOI
Konosuba Show me the money The mc is awesome - her player avatar is ugly The janitor is not a hero LV999 Villager
Sendai Yuusha wa Inkyou Shitai The God Slaying Hero and the Seven Covenants The novels extra Latina the sword princess
Tsuki ga Michibiku Isekai Douchuu idk if this counts though. the mc IS average looking but the world he's in views average as absolutely horrid because everyone looks like a model
Tensei Shoujo no Rirekisho - Not sure if MC is ugly or not but people have described the MC to look like "a dead frog". Omniscient Reader’s Viewpoint - MC is probably average but he gets called ugly by everyone.
Boku wa Tomodachi ga Sukunai - the MC gives other people the impression he is a thug, and his reputation just makes it worse. Kumo Desu ga, Nani ka? - the MC is a giant spider. The manga makes her look kinda cute, for a spider, but spiders are ugly anyway. Other characters usually react with "kill it with fire!" or by running away.