Have you even played The Sacred Stones,The Blazing Sword,Path of Radiance,Radiant Dawn and/or Awakening?They have themes that beat the main theme a hundred times over.Even try listening to The Prince's Despair.It's not even as good as some Id remixes.Seriously,play your Fire Emblem before you judge it's themes off the few in Brawl and 4 3DS.Fire Emblem's only good theme in my opinion is it's main theme. :/
I'll agree with a bunch that were already said, namely Xenoblade, Bravely Default, various LoZ titles, Kid Icarus and Fire Emblem (agreeing too that Sacred Stones had some neat tunes in it). Paper Mario: TTYD is pretty great with its music as well imo.
I am partial to various Pokemon game soundtracks too, but I wouldn't put those right at the top, just near it. That said, Miror B's themes are amazing.