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.
It’s had an excellent fan translation for years, I hate to think what the commies at NoA would do to a story like that today. At this point whatever weird niche Japanese shit you like never getting an official western release is probably the best case scenario.