Before I start I will preface this post by saying that overall I liked the game a lot. But nothing is perfect, and pointing out a game's flaws doesn't mean you don't like it.
I will also note that I beat endings A-E, but I didn't get most of the minor ones or complete every single sidequest (done 90%) or archive (I think about 70%?), so I might be objectively wrong about some things, so feel free to call me out if so.
Basically I will summarise my biggest disappointment in that the game seems to set out to accomplish a lot plot-wise, but doesn't achieve as much. When I beat endings A-B and starting route C/D I was excited. I was expecting to know about Adam and Eve and Copied City. Why do these machines look exactly human? Why are their powers and abilities so unlike anything else in the world? Adam created copied city, it didn't seem that regular machines can do that! And Eve has Cult of the Watchers emblem on his chest?!
Turns out it's nothing. They're just machines that happen to look like humans. How could a bunch of mindless desert bots melt into Adam? Who knows. The pure white tower is also a machine creation despite being so utterly alien and to anything machine (and actual alien) related and containing impossible space. The Terminal is an obvious send off to Manah and Watchers with how little girl's voice becomes adult male's, yet nothing comes out of it either, it's just… dealt with. When you're finding the keys to the tower, the names of recovery unit being written in "angelic" and the names themselves seem to hint at abnormal nature of it all, yet it seems it's just a red herring of sorts. The whole thing about YoRHa project being repeated over and over again made me think there's someone or something pulling the strings of it all behind the scenes. The "Yonah is the last living human and is on the moon" hints stay hints as well.
After all of this I get the impression that the game should've either be twice as long, or actually a bit shorter. The whole 2B/2E, 9S and A2 story is really amazing and I believe it can carry the game by itself. The revelations that both aliens and humans are long dead and whole conflict ultimately being meaningless are strong by themselves. But as it is, some things feel like cheap hooks that make you think there's more to the game. As beautiful as ending E is, in the end it is just a credits roll with tweaks. And "Eve is related to the Watchers" feels like a blatant "shot for trailers to get people hyped".
Again, I really enjoy the game, so I hope you guys won't take it the wrong way or think I'm just shitting on the game for no reason, I didn't intend this post be that. I just had some less than pleasant impressions I wanted to share.