I don't usually have
that one favorite character as it also depends on context and for what reason this character became a favorite.
In terms of character development and personal closure to that character's history, it's most likely
Shichika Yasuri from Katanagatari.
You'll encounter him in the first episode at his blandest and most socially untouched state, he is unable to understand humans and isn't even able to tell them apart. With each episode, you'll get introduced to him as a personwhilehe his introduced to how the world works and consequently about love, affection and understanding that he has something to fight for. The more he understands, the more complete he becomes, which stands as an antithesis and contradiction to "just being a sword and tool" for someone else's ambition. At the end of his journey, he lost and gained something at the same time - and became his completed version although with the constant feeling of longing. That's all I can say without any explicit spoilers.
Close second might be
Kakeru Kurosawa from Onani Master Kurosawa, if we talk about character faults and the ability of personal redemption which is core for more serious coming-of-age themes. Other examples of this theme contributing greatly to a character's popularity are Simon from TTGL, Subaru from Re-Zero, Scar from FMA or Ishida from Silent Voice.
But I chose who I've chosen because the manga left a deep impression on me although the topic may scare people off or they denounce it outright as some ecchi pervert's delusions. The MC fucked things up, lived inside of his delusions, was insecure to the core and deeply hurt because his one-sided love did not come to any fruition. A coward, an egotist and egoist, or simply: an immature kid with a god complex. Even when he had the courage to step forward to admit his faults, he was bullied in return and took it as part of being the one who started it all. The bullying never stopped until graduation and he lost everything he had built up so far. Usually media rewards a good act with good results as a means to educate people to always do good, this manga took it to the realistic extremes and ran with it. Many panels of this manga will stay edged into your mind as long as you exist and will also shape your life and mindset to do what is right and to better do them early rather than late. The MC was given a good ending at the end of it but will never mend the relationships that costed him in order to get that far. Some things just can't magically repair themselves even with time and effort.
The third and last one I would like to mention is purely because of being fan-favorite and liking them because you like them:
Misogi Kumagawa from Medaka Box. He is so popular, he became the poster-child of the series and when speaking from behind-the-scenes, without him the manga would have been canned long time ago. He became the Final Fantasy of Square in 1987, saving and kickstarting the series he was put in.
There are many qualities to him, mainly that he does not function like any other antagonist (or even any character within his own manga when he first made his appearance). He is odd, he is contrarian, his words are lies or statements that will become lies the longer you wait. He is also blunt, his words hurts, his words may be even truer to the wishful thinking that the main characters sometimes spit out. In the perspective of the reading audience, a manga character can only make an impact by the following: their speech bubbles, their appearance, their actions/personality and their reputation among other characters of the same manga. He stands on top of all these factors as he is the sole unpredictable force that pushes the narrative to however he likes, even disregarding common tropes that was believed to be the untouchable status quo. His bracket speech bubbles can only exist in a manga, it's near impossible to adapt that into anime, much so confirmed by the staff that worked on the first two anime seasons. People, me included, like him because he
is HIM.
