One idea being because of the Controversial Stuff that it had to offer, though that can easily be censored, and it wouldn’t hurt for an English Version of Mother 3 to be Rated T for Teen like the other Earthbound games already are. Another possibility is the fact that the game released quite late in the GBA’s lifespan, it was even one of only 2 first party GBA games to release in 2006 (coincidentally that’s the year I got hold of that system myself), the other being the first Rhythm Heaven game (of which was also Japan exclusive).