My personal opinion is that Nier Automata shines in its artistic design. Character design, combat animation, enemy design, soundtrack, UI (and the fact that it's a meta-UI that also exists within the game), level art design, the camera work and the way forced perspective is used across the game, the choice to use bullet hell mechanics, the way the story is presented (I'd argue that the game hasn't to be "played three times", since the actual story is different even if the first two acts cover the same events), and finally, ending E and the fact that the game breaks the 4th wall and presents the player with the same choice that the main characters go through (arguably the strongest philosophical aspect in the game).
It is also a game where all these art considerations take precedence over pure gameplay, and that's what makes it unique.
How is (spoilers follow) the choice of deleting your save file to help another player through the credits bullet hell the same choice that the main characters go through?
Also much of the second playthrough is completely unnecessary for what it was trying to accomplish with the story. The same thing could have been accomplished many different ways without having you retread the entire first half of the game.
> How is (spoilers follow) the choice of deleting your save file to help another player through the credits bullet hell the same choice that the main characters go through?
There are many instances of 2B and 9S "deleting their save file" to help others. For example during the intro sequence both 2B and 9S nuke each other to destroy the giant factory robots. I believe 9S is the one that didn't get backed up before that, so he essentially deleted his "save file" to help save humanity.
And just like the main characters it isn't like "death". You can still play again. But you've lost a set of "memories" that you can never get back. Just like 9S will never get back those memories and experiences he lost from the beginning of Automata.
The androids make a choice whether to help some remote, future civilization they'll never know, or trying to go on with their own life. Which is kind of the same thing you do when you delete your save: it's almost impossible to complete ending E without outside help, and deleting the save file afterwards is a selfless, sacrificial action.
As for the effects of the second act of the game, I was just stating the fact that it's a heavy-handed artistic choice, like more or less everything in the game.
It is also a game where all these art considerations take precedence over pure gameplay, and that's what makes it unique.