Honestly... I'd probably say Demise. If only because he never really made himself known until the very end of the game. Ghirahim was great in terms of personality, development, and challenge. I was disappointed that he wasn't the main villain. Fighting Demise after chasing Ghirahim the entire game just seemed a little... Anticlimactic.
Don't get me wrong, I loved Skyward Sword. I just wish that Demise himself had played more of a role in the game (not in the form of The Imprisoned) other than during the last ten minutes or so of gameplay.