So I just finished the game and had some alternate story ideas. I'll share mine and I'm curious to hear other people's ideas. These are just for fun, so don't get too riled up. I'm a sucker for dark endings.
(Spoilers ahead!)
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Mineru was a traitor all along and was conspiring with Ganondorf. She was jealous of Rauru getting to be king, and when he marries Sonia she becomes king and has more power over Hyrule than Mineru. In the cutscene where Ganondorf kills Sonia, it's Mineru who does it instead. Link only learns of this at the end, when mineru leads him astray at the bottom of the depths where Ganondorf is.!<
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After defeating Ganondorf, Zelda does not transform back. She remains a dragon and wanders off into the distance. Link is saddened by this. The ghost of Rauru sees this and tells link to cut open his hand. His secret stone was inside, and link eats it, becoming a dragon himself. He flies into the horizon to be with Zelda as dragons.!<
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Another idea for Mineru is that, instead of being a traitor, she's actually the Twilight Princess, Midna in her Twili form. Instead of the Owl mask, she woulda had her Midna mask (which looks like a sage mask!)!<