This is alright. I'm not as passionate about CT as most people but I understand why it would be number one, so I have no qualms. I haven't played BotW for more than like 2 hours, so I have no opinion on that front.
Automata is definitely a flawed game, but it goes back to something I learned about the original Nier: it's not always about what's "the least flawed", or the most polished or well-rounded, sometimes it's about what's INTERESTING and what speaks to you. There are "better" games than the two Niers in multiple areas, but it's those two games that have stayed with me, flaws and all. I'll never forget when I saw Ending D in the original game, it's one of the few moments in any game that managed to make me cry, I had to go sit down and have a think afterwards. In terms of story and characters (and music) I legitimately prefer them to any Final Fantasy, Chrono, Breath of Fire, Persona, etc. It's true that a lot of fans prefer the first game's story and characters, and I kind of do as well, but Automata has a lot of merit to it and a number of things it does better beyond the gameplay and graphics.