Now, I never played Mother 3 because I'm not that good at Japanese and I've never arsed to try the fan translation because there's always a new rumor about how it's coming out soon for the Wii/Wii U/Switch, but from my understanding...
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Loses most of his family early on, brother then later gets killed, revived as a cyborg Nazi, has to kill him personally at the end because of Pokey's meddling. Somewhere around there?
Yeah, sounds dark, but painted over in that Americana art style and the more overt references like Nazis are replaced with a faux Nazi clan. Like Earthbound with its blue Ku Klux Klan. The symbolism is still there and dark and whatnot, but Ridley is just too straight-forward. He kills and eats people, then brags about it. And if we ignore the manga and just stick to the games, he still kills people in the beginning of Super Metroid and gets all sorts of deformed in Fusion. It's the graphic imagery that I'd imagine Sakurai would have trouble circumventing, rather than deeper plot issues.