Just some food for thought, what about a dual story?
My idea starts off in a slightly darker universe of OoT, in that the King doesn't trust Ganon in the first place. Eventually, in an ambitious move, a coup is launched and Ganon is forced off his throne, leaving the King (name?) of Hyrule as the sole significant kingdom with any form of military in Hyrule. As power tends to do, it corrupts, and the King eventually becomes more evil, and tries to seize the power of the Triforce for himself. However, around this time, a small boy from Kakori Village stumbles out of the forest...Into the arms of the royal guard. Eventually realizing that he is too corrupt to release the master sword, he eventually forces Link to take the sword.
Que Ganon, who has been hovering around stealthily, make a play for power by seizing the power of the Triforce for himself. Of course, he isn't fit for it's whole power, and Wisdom heads into Zelda, who likely doesn't live in the castle. If she does, she hides the fact that she has the Triforce. If she doesn't, her mentor keeps it s secret somehow. And the Triforce of Courage resides within the boy who pulled out the master sword, who is trapped by the sages like in OoT for seven years. The king, however realizes what the sages have done, and has them sealed away into their respective temples.
Ganon escapes into the night, utterly destroying portions of Hyrule castle and the nearby village in his dash to escape, high on his new found power. Zelda, meanwhile realizes her destiny, and begins plotting.
Seven years later, a surprised Link wakes in a chamber of soft light, staring at a beautiful princess, asking him to embark on a quest. Likewise, Ganondorf, emerging from the desert from whence he had been hiding, brutally slaughters the main base of the Gerudo in the desert.
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Wow, that idea kind of built on itself. I didn't realize how deep that plot could go, but it flowed out on it's own as I kept typing...
And the TL
R version expanded itself too. Ops...
TL
R version(with new ideas):
King of Hyrule seizes control of the Gerudo from Ganon, who hangs around, hidden by his magic from the King.
King becomes corrupt, eventually trying to steal the powers of the Triforce for himself. A few days prior, Link had been captured by the Royal Guard, and is forced to remove the Master Sword from it's pedestal.
Ganon, sensing an opportunity, steals the triforce of power. This action, however, sends the triforce of courage to Link, and wisdom to Zelda.
The sages, taking action at the last second, kidnap Link and seal him for seven years. Zelda (if she lives in the castle still) hides the fact that she holds a portion of the triforce from her father, or if she does not, her mentor does, bides her time until the destined Hero is ready to save the kingdom.
Seven years later, Zelda wakes with a start, the Hero is awake. She travels to Kakori village, and the Deku tree, dead for seven years, suddenly catches an azure flame. At the ashes, Zelda finds her hero.
Meanwhile, in a shocking and brutal attack, Ganon destroys the King's gerudo fortress, slaughtering those within it. Ganon had been previously training in using his newfound power, and has now set his sights upon the throne of the King of Hyrule.