http://www.mangago.me/read-manga/sick/
http://www.mangago.me/read-manga/tsukiatte_agete_mo_ii_n_dakara_ne/
these two are more teasing than anything super hardcore
http://www.mangago.me/read-manga/itonaga_kun_no_koi_no_ito/
http://www.mangago.me/read-manga/geu_kkeute_issneun_geos/?8weF
http://www.mangago.me/read-manga/smells_like_green_spirit/
http://www.mangago.me/read-manga/mobius_strip/
This one has good development, complex characters, and an (eventually) healthy relationship. Ngl, I like stories like this for the guilt trips when a character realizes what they did was wrong, and this one definetely delivered. http://www.mangago.me/read-manga/cosmic_boy/
Like http://www.mangago.me/read-manga/never_understand/? It exactly as you describe, the MC is the ugliest boy in the school who got bullied hard, and the ML is the most handsome boy at the same school. I remember crying while reading this manhwa, but the story ends well iirc.
Uh, I checked the comment section of this manhwa and got reminded that there's a sexual assault/attempted rape scene.
Anyone know of any bl mangas where the main character is a bully victim, and either the romance happens between him and the bully or a third party saves him or something? Rather nothing with rape, but where you feel super sad for the Mc and eventually he gets a happy ending or smth?