I freaking love both SoTN and Super Metroid. Two of my all time favorites. The action-RPG blend, and sense of exploration, discovery, and character growth are excellent for gameplay. And the music and environments in both games really give a great atmosphere to both games.
But if I had to choose one or the other, I'd go with Super Metroid. I really can't say any one thing about it that's significantly better than SoTN, I just prefer it if I had to choose.