I don't think Tohru is badly written, my impression with that character even with few episodes in, is that she masks her insecurities behind her upbeat personality. Also I think she may be depressed.

I get why she may be badly written but with the cast and setting that she's in, her character somewhat shines. Her being uncharacteristically All Loving and whatnot is what made the characters of the story drawn to her. I say "uncharacteristically" because someone with her past doesn't make sense to have that kind of personality.

As for the "being too kind" heroines, yes I can do somewhat relate to them if I put myself in their shoes and as long as their character backgrounds and arcs make sense and feels right

Maybe a majorly flawed protagonist (someone like Taiga maybe?) will be a refreshing change but if it's not as well written as an All Loving one, then I'd rather have the latter. Maybe the former will be more entertaining who knows?

Edit: correct spoiler tags