Busu ni Hanataba wo.

same trope - shoujo, school life romance. the main girl is a shy, timid person who lacks confidence. The popular guy in school befriends them and romance brews. 

school life, romance, shoujo. The main girl is shy, deep insecurities, but a main guy character notices her. he befriends/watches over the girl and teaches them how to socialize. 

Don't even bother watching Busu ni Hanabata. If you're craving the "Conventionally Unattractive Heroine and Popular Ikemen" pairing- Hananoi-kun is far better. The character designs are unique, and the FMC is not hopelessly dense or as self-obsessed with negative self-commentary. Each character is genuinely present, aware of their own flaws, and struggle in a beautiful journey to overcome them whilst conveying their truest selves to those they care for. It's a love story worth watching. Both of these have: High School Setting "Ugly" female lead Popular boy (actually very attractive) Main character who's dense about romance 

If you want a lighthearted romance but with more interesting and meaningful storytelling- this one is pretty good! It's super similar in the pale colorscheme and ugly girl/popular guy pairing. Much like the MMC, this one is very kind, down to earth, and golden-retriever like. The characters in this show have worries that come across as far more realistic and relatable than the flat, tropey stereotypes seen in Busu ni Hanataba. Both of these have: Slice of Life Highschool Easy going, slow paced story Pastel color scheme Ugly girl lead Popular boy counterpart 

In both anime, the popular and beautiful protagonist is drawn to someone unconventional in appearance but deeply kind and sincere at heart. school life, shoujo romance.