Hi, I recently played NieR Automata and absolutely loved it!
What I liked the most about this game was the story which, long-story short, is very complicated, obviously. Main aspects of it was the ambiguity of all the characters and very thin borders between known subjects as what is right or wrong, the good and evil and stuff like that. But the cherry on top was the relationship between the two main characters, which wasn't exactly ... optimistic. Their whole relationship's base is pure despair of unability to change anything so it grew to be something bordering from love, even obsession, to anguish and hatred, with murderous intent. As I said, it's very complicated but I am trying to give you the general idea.

So, what I am looking for is a manga/anime/whatever with a love/hate story but not your typical shoujo one. I want to see the inner turmoil of the characters trying to make sense of themselves and the other partner in the relationship, trying to fight against themselves and the negative emotions within them for the sake of their own happiness and the future. (well that got philosophical, didn't it?)
It doesn't necessarily need to be a romantic relationship, although that would be appreciated.

Bring on the angst! Yay! I feel like I want to suffer a little bit so yeah, I'd love any suggestions on this matter! 😁

Hana Yori Dango - The leads have the very definition of a complicated love-hate relationship.

Flowers of Evil
Aku no Hana
Oyasumi Punpun
Watashi no... Megane-Kun
Dokuhime perhaps...

I second Watashi no...Megane-kun and Flowers of Evil.

Sakura-Gari - I don't know if you are willing to read M/M, but this work is Watase Yuu masterpiece. Seriously, it's incredible: dark and complex as they come.

Bokura no Koi wa Shi ni Itaru Yamai no You de - didn't read it, but it seems to fit your criteria?