One can argue that the game is designed that way, but I can safely say that the first ending (A) that I've seen now just doesn't deliver on its own.
The game does remind me of Panzer Dragoon Saga, in the sense that it offers a bleak world where people struggle to survive, and you have several side quests that don't end well, much like in Panzer Dragoon Saga. You don't get the sense that the protagonists are on a glorious quest to save the world. Instead they're stuck in a seemingly endless war, and staying alive is an achievement in itself.
However, Panzer Dragoon Saga was consistent in its tone. NieR is different because there's a lot of metagaming going on, and as such I feel it doesn't manage to have the same immersion PD Saga had. The game does uses that to its advantage as well, making the story unpredictable. Several events really made me question just what was going on.
What I also found odd is that the game establishes very early on that emotions are forbidden for androids, much like it was for drones in Panzer Dragoon. But the rule is forgotten as soon as it's introduced, as all the androids show emotions and act very much like humans do... If anything it's only 2B who seems to try to adhere to the rule, if only to shield herself from getting hurt.