It's quite easy, all in all, the game featured questionable content. Panty shots of underage girls, and them in gravure-like bikini shots etc. Even if they altered their age to 18, chances are it would've earned an M-rating in the West.
Meaning, it would not have been sold in a lot of places and I don't think Nintendo wanted that. So they opted for this. And, while you could argue that the alterations could've been done better, most of the time I see people not getting what they want; "sexualized under-age girls", and trying to defend their position somehow.