I think this game handled the whole grey vs grey morality better than NieR Gestalt/Replicant (gonna refer to as Gestalt), where you're constantly bombarded with both moments of machines acting like humans, at times expressing emotion, a will, and frustrations.  But then you get your chain yanked at times and sort of reminded you're stuck in this seemingly endless war between androids and machines.  It works a bit better than the "Shades did nothing wrong" from Gestalt where when you're shown the side of the shades, you see they're mostly innocent or just misunderstood.  Not saying Gestalt is worse because of it.

Then on the side of the androids, you're constantly told the machines are your enemy, they can't contemplate any sort of human behavior, and any attempt at so is just them imitating it.  This gets somewhat backed up in archive files you find saying when machines were trying out stuff, they would constantly repeat failures (mostly in regards to politics).  But then you're shown robots like Pascal and his entire village, who absolutely do not want to fight or hurt things, or the robots you see as 9S contemplating their own existence and the one that ultimately realizes the futility of living and ends itself.  And even then after all that, in the case of Pascal's village, some machines suddenly turn violent and start cannibalizing each other.  You're sort of left guessing if machines can learn and develop free will or if it's just imitating.  Gestalt pulled the wool off your eyes completely after you got Ending A, and Automata gently sort of lifts it off as the game goes on.  I probably missed some details or misunderstood something oh well.

This game also makes Gestalt even more grim by showing you that because of what happened there, you in fact 100% and irreparably fucked over all of humanity, and because of Nier completely erasing his existence to save Kaine, the blame was solely put on Popola and Devola, going as far as making sure every single Popola and Devola android feels guilty for what the two in Gestalt did.  In hindsight it sort of makes what you accomplished in Gestalt all the more questionable, since not only did you guarantee the humans going extinct, but two people you cared about deeply took the blame for what you did.

The only part of Automata I'm really iffy about is the whole "aliens invaded".  It feels a little bit ass-pull, but I'm kind of better off not thinking about it too much.