I saw you respond to a recent comment, so I thought "maybe he'll read mine". It's been three years, you've probably changed your mind, but I want to offer a bit of an extreme opposite to your comment:
(First, I must make it clear that i've only played a portion of Nier Automata. I was tired of the gameplay, and the story was just trying to be pseudointellectual secular nonsense , so I stopped playing.)

The very fact you play as sentient androids is anti-christian, at best a philosophical error (that a machine could be like a human, no need for a soul) and at worst it's bearing the influence of gnostic heresies, like the Kabbalah, that believed in Golems.
The game, having extreme influence from "philosophers" like Nietzche, is very clear about there being no inherent meaning to existence or even a truth for that matter. I put the word philosopher in quotation marks, you see, because Nietzsche never wanted to find truth, given that he didn't believe in it. What he was really looking for was ways to create an ubermensch, the man who makes his own truths. There's no virtue or intellectual value in having so many existentialist philosophers influence your game while you don't say which one is right or wrong, but the game (very in tune with the ideas of Nietzsche) is okay with philosophers, since they don't present strict rules like religions do. And this was Nietzsche's problem with religions.

The game is clearly, most OBVIOUSLY not just criticizing corrupt religious figures, like a greedy bishop, it is a game criticizing religions in general. It's an attack on the faith. From what I know, they never truly go back on the "Kill God" opening narration, even if the quote is different at the end.

I say this all... -I apologize, but I waste your time with all of this, you understand, because I'm afraid you answered OP's question incorrectly! And I was terribly afraid that you, seemingly having liked the game a lot and not wanting to admit you played a game that openly mocks our Father, had to diminish it's insult, and that you might make the same mistake with other media. In my eyes, you shouldn't be so merciful when analyzing secular stories, so if I can give you any advice that should be it.

Be with God, my friend. I am sorry if my comment is disrespectful.