Shin Megami Tensei IV. Still the best 3DS music - industrial, dark - well...something you wouldn't find in most fantasy RPG. "Tokyo overworld theme" is something that makes you calm after fighting bosses. It's peaceful and refreshing.
Fire Emblem: Awakening would be the second. Though it has fantasy-themed music we could find in most RPG, it suits the game well. My favorite is "Conquest/Conquest Ablaze" and "[Id] - Hope."
Etrian Odyssey IV would be my third favorite. Yuzo Koshiro is a genius. The battle theme (i forget the title, something "is my pillar" is all that I can recall), and "Radiant of Ruins" take my heart away.