So for Nintendo's titles... honestly the only one that jumps to mind as fitting all of these criteria is Metroid: Other M. It's a rare Nintendo game with a big focus on story, Sakamoto went out of his way to talk about just how personally involved he was with the narrative and how he stayed up to storyboard and direct every single scene. He also forcibly oversaw the English voice direction even though he didn't speak a single sentence of English at the time. And what we got... was a game whose mother metaphors are subtle as a brick, is without a doubt one of the most sexist games of its generation (to the point where even most dudebro reviewers picked up on it) and the aforementioned voice direction made Samus sound like a robot.
Besides that one, Nintendo's list of games just doesn't really have that type of high profile failure, and I think a big part of that is also because pretentious games come out of a very specific type of culture of videogame pitches that Nintendo kinda doesn't have. They used to stumble with it (Retro almost went in that direction because fuck Jeff Spangenberg) but Other M was their wakeup call to avoid that sorta thing in the future.