After long deliberation, I have finally come to the conclusion that Skyward Sword is the story of Fate vs. Choice. It is the battle between what was designed for someone long ago, and how they will try to change it, and if trying to change it is a good decision at all.
For example, the Batreaux quests. In the Cawlin's Letter one, you can choose to either make Pheoni (aka ???) happy or Pippit and Karane happy, but Cawlin is fated to have his love be unrequited no matter what. Also, the Peatrice Quest is also a great example. Peatrice can never be with Link, but you can choose wether to break her heart and make her father happy, or make Peatrice happy and leave her father distraught (its worth mentioning that Peatrice would be heartbroken anyway after Zelda and Link reunited). For once in the series, actions truly have consequences, but even though you can choose how the events play out, there are still many things that can never be changed.
The exact same thing can be said for the Lanayru Desert, and how the first Demon war turned it forever into a wasteland. Whenever you use a timeshift stone, you are returning to a doomed land, and though you can change how it turns into a wastleland, there's no changing that it does. In the games climax too, there is this element of hiding from the inevitable. While Zelda and Link accept their previously decided roles in Hyrule's history, Ghirahim cannot, and tries futiley to change the future by returning to the past, and fails, like Link and the Lanayru Desert.
Though elements such as these are present in games such as WW, the ideas shine most brightly here, creating a beautiful conflict and an internal struggle that may be the reason why so many people prefer
SS Princess Zelda to many of the others.
So what do you guys think?