The decision that this game asks of you in ending E is near perfect for me. I know it's basically the same thing as the first NieR, but it still worked.
For me this game was ultimately about loss and sacrifice. Every moment prior to ending E results in loss or requires sacrifice. You're swimming in it by the end. And then Yoko Taro asks that of the player themselves in order to help another complete stranger. This game made me feel a looooot of stuff. But I only cried when the credits were rolling, and the chorus of voices came in as all those helper ships came around and I finally got to see the final ending. It feels hopeful, just like ending E makes the player feel that there may be hope of ending the death cycle the main characters are trapped in.
Worst part: I selfishly kept my save. I literally couldn't sleep. I stayed in bed for like 2 hours, woke up at 3AM, finished the game again and deleted my save. I don't know what Yoko Taro did but I've never felt a real sense of regret from a choice in a game. It was really special. Though I still think my initial decision makes me a bad person.
Best part: The game only thanks you for playing if you delete your save, at least that's what I observed. (could have missed it) and I thought that was an amazing touch.
Edit: I left this game basically hating everyone except A2. 9S and 2B are sympathetic, and I chose to give them another chance by getting ending E (which I do really like) but they're not good people. I liked them as characters, I hated them as people. I think 2B hated both herself and her job but she still conducted her duty by murdering not only 9S, but other YoRHa units. By doing this she also locks in 9S' fate. He's basically in a permanent state of adolescence. 9S fails to understand what he learns and chooses to reject reality ultimately leading to his insanity and choice to conduct a genocide against machine lifeforms.
The only person who changes for the better in the entire game is A2, who, through Pascal, learns that her path (which initially, is similar to 9S') is not the right one. There are other options, and other choices. Her purpose by the end of the game is to protect, not destroy, while everyone else either chooses that violence and destruction are the way forward, or can't do anything but destroy because they can't figure out how to stop.