Would you like a story where the MC's good points are only his good looks? I don't really understand why the MC being athletic is a cliché.
It's cliché because, first, the good looking thing basically poped up after him cuting hair and the reactions were so exagerrated (it's seen a lot of time in manga and even in movies/books not related to manga).
It's cliché bc many authors just make random characters around say "MC is the pretiest person omg" whitout actually make a design that could be showing that obviously. Tbh, the artsyle is pretty to me but the mc doesn't particularly looks more gorgeous than the other classmates.
Same with the athletic hidden skills lmao: at the start of the chapter mc said himself he doesn't know his capacities, that he always tried his best to get was average grades in p.e, and dude never praticed in
YEARS (bc of the bully).
He was literally in
kindergarden the first time he ran so fast that he won a price, bro is now in
highschool and never even practiced or anything (last time he ran "fast" was under the rain to go meet the bully at night and after that dude ended at the hospital 💀) and you gonna tell me it's not cliché to just make a character suddenly skilled at something they barely tried? Even if he was talented to start with, it needs practice.
I think the whole thing so far is taking shortcuts idk what is not cliché about that, you can find the same things in other mangas with other themes (like, injustified powerup: shounen use that a lot, suddenly looking good even tho the design is not that special and they just changed one thing: many shoujo do that too). If it's not cliché it's poorly written then.
He could totally be handsome, gain many friends and even be super good at sports but here it just feels rushed/too easy for no reason and that's why it's cliché.
So no, the problem is not even that the mc looks good. Adding "good points" to the MC is easy if it's just how it's done.