IGN has come up with there own list of conspiracies about Skyward Sword. Gathered from the GDC trailer that was released, they were able to come up with some stuff that they believe maybe in Skyward Sword. They believe that it maybe Ganaon will be the last boss to fight, “It’s probably also safe to assume that Ganon will be the last boss fight (as no console Zelda game to date, outside of Majora’s Mask, has featured a different final boss)“, also they are hopping that Sheikah tribe or Sheik play a roll in the game, since the harp that can is seen on the controller in the GDC Trailer resembles Sheik’s own. They also suspect, just like everyone else, that the mystical character in the game resembles Vaati from The Minish Cap. They have also identified some other aspects such as enemies, bosses or mini-bosses, items and so on.

Originally a Minish himself, Vaati used the all-powerful Minish Cap to gain vast powers and force his way into the human world. As this game takes place early on in the Zelda timeline (perhaps earlier than any Zelda game to date — another theory of ours we’ve yet to confirm), it’s not out of the question that this mysterious sorcerer is, in fact, either Vaati or some incarnation of Vaati. They not only share a similar look, but also a clear affinity for the color purple.

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Source: IGN