I do think people make a lot of assumptions about Sakurai like "he wouldn't do this" and whatnot, which can absolutely color people's speculation. That said, there are certainly some extrapolations we can make based on past comments.Honestly, I don't think that's really a deconfirmation or anything. It doesn't help, but not meeting in person doesn't mean they couldn't had interacted in other ways.
I mean maybe I'm missing something but I don't think Sakurai visited Square Enix HQ frequently while working on Hero, to say something.
And while Yoko Taro is of course the creator, even if he gave permission to Sakurai to use 2B in Smash, the final decision is up to Square Enix as a company because they own the character. I mean, Nomura and Sakurai are friends AFAIK and yet we don't have any FF7 spirits when Nomura was the main designer of that game.
Also, obviously it wouldn't be the first time for Sakurai and Nintendo to negotiate for a Square character, so if they want 2B (or Geno, Lara Croft, etc) I guess they would probably start things talking with someone else at Square Enix, probably a high executive like Yosuke Saito. It doesn't have to start with Yoko Taro himself.
For example, the K.Rool rebuttal with his creator not knowing about it. The reason that doesn't really work is the guy had nothing to do with the franchise by this point, he's a first party character, and the creation is entirely on the western side. We already know that Sakurai has more trouble working with western developers due to the language barrier based on his comments around Kirkhope. So that right there is a massive knock against the comparison.
As far as 2B is concerned, we assume Sakurai would want to contact Yoko Taro first for one reason; he's a big fan of Nier Automata. People kind of see him as this Weird Al-like figure that's not only getting permission from the original creator just to get them in, but also out of respect for the products and his absolute love of video games in general. I think it's a fair assumption, but that's not something we can know for sure. He absolutely could have just talked to Saito, who may have tried to push the character in the past and Sakurai accepted while wanting to meet the creator later (which he likely would have wanted to do whether 2B was in or not).
Basically, this lowers 2B's chances based on a lot of (valid) fan assumptions, but it doesn't kill them outright.
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