I'll keep this as spoiler-free as I can, but it really is a great game, I've cleared it. Anyway...
It all comes down to the Magypsies. They're aliens that look like drag queens...Mother games are weird.
You change the name, it's censorship.
You leave the name, Twitter explodes about an "anti-Romani slur."
You leave the sprites alone, it's anti-tranny stereotypes.
You change the sprites, it's LGBT erasure.
Nintendo's in a bind. So they just don't release it, because dealing with the "give us Mother 3" crowd is better than dealing with the SJW Twitter mob.
I wouldn't be that surprised if this was the reason Nintendo hasn't released it. But at the same time I also have to think that many members of the latter are also part of the former group, and just as even the SJW crowd told Kotaku off for their article about Stray, I think they would mostly look the other way for Mother 3.
Of course, Nintendo wouldn't want to take that chance.