This was a tough one cause it had a lot of my favorite 3DS games in the list.
FE Shadows of Valentia was amazing.
SMT Devil Survivor 1 was great
Bravely Default and its sequel were great too
But because of SMT IV/Apocalypse - that has it all beat, such an amazing game overall, story, music and gameplay - so SMT IV/Apocalypse gets my vote.