These are what we call the 'YMMV items.' Things that some people find in this work. We call them 'your mileage might vary' because not everyone sees these things in the same way. This starts discussions in the trope lists, a thing we don't want. Please use the discussion page if you'd like to discuss any of these items.
Junior, in his feelings of terror and helplessness of what it will mean if he's uncloseted. He ended up making some stupid and careless choices that cost a great deal to friends, loved ones and family. The thing that makes him so damn sympathetic in all of his stupidity, is knowing that he's still a kid who has absolutely no idea how to handle the hardest cards dealt him, and has had to improvise in all his fear.
Hanbei, in losing his parents, in being rejected by his natural extended family in Japan, and having that dark violent streak to keep under control.
Bowser, for having a father like Rufus. How horrible.
Mary Sue Classic: Hanbei, even with his informed flaws, is still beloved and respected by all. The creators are already aware that Hanbei skirts sue-dom.
Stoic Woobie: Jojo. Honestly, both he and Junior exercised moments of poor judgment, but you end up sympathizing with them both. Every description of every blank stare and stoic word Jojo gives after their breakup, feels tragically chilling. Interestingly, Jojo's sympathetic nature multiplies when he finally drops his stoic façade once he discovers Junior so badly beaten on the school rooftop. It's then that you realize the stoicism was largely a façade, and that he was hiding his real feelings inside. It's apparent they both still love each other, but it was their shattered trust that drove them to estrangement.