I think you can write a book about all of the idiots in anime, especially in the shounen genre. There seems to be a plague of baka protagonists that capture our hearts. Here are my top ten! As usual, I tried to choose characters from a variety of genres—however, some definitely use this trope more than others. Note: Some series have more than one character. May include spoilers.
Rock Lee
Naruto
The original bushy-brow, Rock Lee lacked the skills to use ninjutsu or genjutsu but perservered with hard work and learned taijutsu. The epitome of a nice guy, his intense but polite nature is charming.
Tohru Honda
Fruits Basket
While not my favorite character, Tohru certainly possesses likable qualities. She’s extremely empathetic, cheerful and overly optimistic. Additionally, she’s pretty spaced out, leading her to be bossed around by other bombastic characters as well as being labeled as a pushover.
Gon Freecss
Hunter x Hunter

Gon the Gullible isn’t praised for his skills in mathematics or strategics. Throughout the series, he’s depicted with his brain overheating when he thinks about something difficult.
Onoda Sakamichi
Yowamushi Pedal
This climber is very shy, unaware and has a bit of a one-track mind. Easily flustered and unsure about himself, it’s easy to find Onoda’s character endearing. He’s also extremely determined and his desire to help his teammates defies all logic, leading him to make some idiotic decisions that determine the team’s success during key races.
Mob
Mob Psycho 100
Mob is one of the most pure and innocent characters in the shonen world. While being immensely powerful, he’s quick to believe others at face value and struggles with communication. Bless this little potato.
Tamaki Suoh
Ouran High School Host Club
Arguably one of the most obnoxious characters of all time, Tamaki’s dramatic personality saturates the show. His flamboyant and egotistical nature serve as the catalyst for most of the show’s plot as well as comedic points. While he celebrates love, he remains painfully obtuse for his own affections for Haruhi, leading for a lot of dramatic irony.
Isshiki Satoshi & Takumi Aldini
Food Wars!

I couldn’t pick one character for Food Wars, so here are two which act as foils in a way.

First we have Isshiki, who struts around the series wearing nothing but an apron to clothe his nethers. His character is surface-levelly laughable and his actions appear idiotic. However, as the series progresses he shows not only his culinary skill but his cunning personality.

Takumi has the opposite depiction. While he wants to be taken seriously, it is this seriousness which makes his character so amusing. His rivalry with Soma is largely a one-sided relationship, and his passionate outbursts have us all face-palming.
Sawako Kuronuma
Kimi ni Todoke: From Me to You
Honest and shy, Sawako is the exact opposite of her ghostly appearance. Her nervousness and anxious nature is relatable for us introverts, and her pacifist but protective nature leads to a lot of self-sacrificing. Ever grateful, Sawako tends to applaud other people’s efforts before her own. She also shares the naive nature of a lot of my other pics.
The Four Dumb Crows
Haikyuu!!
You know I was going to mention Noya, Hinata, Tanaka and Kageyama in this post. It had to be done. There are a couple episodes devoted to their stupidity as well as accent scenes like this one, which always leads to plenty of laughs.
Erythrocyte / Red Blood Cell (AE3803) / Sekkekkyū
Cells at Work!
This little red blood cell is always getting lost! Quite literally in the wrong place at the wrong time for most of the series, Sekkekkyū-san is determined but scatterbrained and she consistently works hard to become as reliable as her peers.