I firmly believe that MOTHER 3 has, without a doubt, the best narrative out of any game that Nintendo has ever published. It is a deeply moving and meaningful experience. Considering Nintendo's preference towards a complete absence of narrative themes in games that they oversee, it's shocking to think that they had anything to do with this game at all. Whatever the case, Itoi and the development team were given a great deal of narrative freedom, and through the fires of hell that were this game's development, they created something truly unforgettable.
In terms of gameplay, I have no complaints. The battle system improves on Earthbound's mechanics in a great many ways: it's snappier, smoother, and much more balanced in terms of game progression. Although simple, the rhythm mechanic takes the typical bore out of watching your character's actions being executed. At the end of the day, though, the gameplay really is just complementary to the game's narrative, at least to me.
However, I can't give this game a perfect score for one particular reason: there is a lot of filler.
The game has a good few plot points that simply go nowhere in the scope of the entire story. In particular, chapter 2 gives pretty much nothing to the plot minus introducing Duster and Kumatora as characters, and chapter 7 is infamously drawn out. And while Itoi's creative direction gives us plenty of interesting experiences and wacky happenings during these sections, it still feels slightly disappointing and mildly boring to play through them.

All in all, it's a spectacular game. I don't know if I'd call it an absolute masterpiece, but as far as games from Nintendo go, it's easily one of the best.