In the process of the Mother 3 fan translation, something utterly horrifying was unearthed. This was the unused background for the final Masked Man fight. It is Purely Unrefined High Octane Nightmare Fuel. At first, I believed in the theory that Lucas kills the Masked Man, before he figures out that it was Claus. This causes some sort of dementia, and Lucas must fight it. That's right. He must fight the dementia brought on by killing his own brother. But in actuality it was only the original background for the Masked Man fight. The plot would have otherwise unfolded regularly. Note that the following video is extremely frightening.
Another example of things too utterly terrifying (apparently) to be put in Mother 3 is the original script of Tanetane Island. Apparently, Itoi himself was behind the change, apparently being too scary for the creator of the series, let alone Giygas and the things that are on Tanetane Island in the game, which are pretty damn scary already. Now that's scary.