When I played this game for the first time earlier this year (as a huge fan of the original), I realized they basically had the same strengths and weaknesses, but Automata was just a lot more polished.
Automata is definitely a flawed game, and it's not "for everyone". I noticed that very clearly when playing it, and understood some of the criticisms I'd been hearing in the two years before I got to playing it. I can see plenty of reasons why people wouldn't enjoy it.
But the first NieR taught me something very important about my gaming tastes: it's not always about what's the "least flawed" or most polished. I have played "better" games, but they're just not as INTERESTING or speak to me the same way these games do, I don't think there is a game that has occupied my brainspace more except maybe the first Dark Souls. Sometimes the flawed but interesting game is more worthwhile.
I'd easily consider Gestalt and Automata to be in the top 5 best games Square has ever published, I honestly prefer them over any Final Fantasy, Chrono, Xeno, etc. Those games are good, some are even great, but they don't speak to me the way NieR does.
I haven't really cared for any JRPG story in the last decade and generally have low expectations for the writing whenever I boot one up...except for Yoko Taro games. Despite its flaws Automata was always at least somewhat interesting and at its best is one of the best and most unique gaming experiences I have ever had. Even Drakengard 3 which is probably his weakest recent project was still interesting enough that I don't regret playing it, and it's certainly more memorable than many other games I have played, for both good and bad reasons.
I have always believed that Yoko, despite being billed as a "niche" director, could have made it big if he was given more resources. I'm glad to see that I was right. It's still insane to me that this game has gotten as big as it has. 5 years ago, Yoko only had a small cult following thanks to the first NieR, now everyone knows who he is.