This is subjective, but as Mario RPG demonstrated to me, a well-fleshed out world and story can be delivered just within the confined universe of that franchise.
Again, for me, shoe-horning in a band of mysterious, questing teenagers and the anime tropes they would likely bring with them (in this case! In another context I might be a fan of questing teenagers and anime tropes) and making their journey the crux of the plot is not a prospect I would appreciate as much as one along the lines of the charming original featuring the characters I already love front and center.
I am sure Nintendo could handle a spiffin game in-house but it would be nice if an experienced Square-Enix team handled it just because they have demonstrated past aptitude and it would be another nice sign of a healthy relationship with a key 3rd party partner. That and they could put in some random Final Fantasy cameo bosses (I AM a fan of some types of shoe-horns).
But really, I just want to see good ol' Geno again.