My personal favorite for flawed reasons is Madoka because I was there for the live reactions to the infamous episode and it was magical watching everyone lose their shit. It was also my re-introduction to anime after being shamed out of it for liking sailor moon as a kid.
I'd also add Yu Yu Hakusho (also by Togashi) to some extent, especially the ending
major spoilers
Yusuke realizing that he has nothing to fight for and would rather go home to be a normal teenager than keep fighting in another stupid tournament just to be the king of demon world (which he never even wanted in the first place) is in many ways the ultimate deconstruction of the shonen genre
It's kinda ironic how much of both of these manga were ripped off by Bleach and Naruto respectively considering how those 2 were considered part of the big 3 shonen series alongside Dragonball