Skyward Sword was released as a 25th Anniversary Zelda game.  It was hyped as being the next Ocarina of Time, I can say otherwise.  Don't get me wrong, it is a great game, but it is not my all-time favorite.  I still prefer Twilight Princess over Skyward Sword, and here's why:

• Twilight Princess has a very connected story-line, and it's very fluid.  Skyward Sword is a mixed bag when it comes to storyline.
• I prefer the mini-games in Twilight Princess over that of Skyward Sword.
• The bosses in Twilight Princess really have a WOW factor, Skyward Sword bosses are more of "meh".
• Twilight Princess's world is very vast and re-visiting them later is fun.  Skyward Sword's world seems limited.
• Midna is more connectable for the player than Fi, especially during one part in Twilight Princess.