Another one for Fullmetal Alchemist here. The manga and Brotherhood anime, I mean, not the first anime (a.k.a. the depressingly bleak spin-off that was riddled with poor pacing and time-wasting filler, fucked over the majority of its characters, not least of all Hohenheim, and had a piss-poor ending in a follow-up movie that made no fucking sense whatsoever). I'm currently writing an essay on Mustang and Hawkeye's relationship just because of how much I've found myself invested in it, even though it's not as blatant as so many other relationships in other anime.
Not to mention that FMA probably has one of the most well-rounded character casts in not only anime, but fiction in general. The only characters that I genuinely dislike (discounting the ones that I just find bland or superfluous, like the Elrics' chimera comrades) are Winry and May Chang (because I don't like their character designs, and I find them annoying characters who just get in the way most of the time).
Even though I think author Hiromu Arakawa could've probably stood to explore the philosophical themes of her manga, since she did apparently research a lot about alchemy as well as drawing from her own life experiences, it does reasonably tackle some things that just may irk at you at certain points (like Edward's constant moralizing over not using the PS to get him and his brother's bodies back just because of how it was made. Look, kid, it happened, it can't be undone, GET OVER IT. Do you want your brother to stay as a hunk of metal forever?).