The problem people have at this step is that they often don't grok the nuance between a sympathetic character trait and a positive character trait. A character being relatable or sympathetic need not come from how good or nice they are, in fact it really often isn't.
One character I'd point to as a case study for this is Mae Borowski from Night in the Woods. She's a twisted knot of character traits usually seen as negative. She's reckless, obnoxious, insensitive, childish, kind of dim, is bad with people and worse with friends. She has zero filter and no dignity, and has a casual relationship with reality at best. But people like her character because these problems hook into people in a deep place where they can see these problems in themselves or the people they used to be. She's almost the polar opposite of your standard bland isekai protagonist, because instead of being a cipher for the player to project themselves onto, the player instead projects the character into themselves.
Theming is important here too, if you have a story where a strong thread is mental illness like Night in the Woods, that's going to draw people in who can relate to those problems. It's also important for the world to actually react to those problems, not really by punishing them or having 'consequences' but creating situations with the character that the reader might relate to, instead of having the character act a certain way and the story just not acknowledge it.
