The CD-i Zeldas wouldn't have been any better if you pallette-swapped Link into Zelda's place. I think since Zelda has a completely different moveset from Link it would make a game with an entirely new feel, much more based on exploration and puzzle-solving. Plus if she could transform into Shiek it would be AWESOME, because then you could pretty much run around Hyrule as a sweet ninja!

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My timeline theory:
Same sword, different day.