Big Name Fan: Inverted with Arin Hanson, a.k.a. Egoraptor, a YouTube personality and Let's Player who was very outspoken over his distaste for Skyward Sword. Many people who haven't even played the game themselves are aware of Arin's stance as one of its biggest detractors.
Before his name was revealed, the GameFAQs community settled with Tracy, and Zelda Universe with Debbie. They still insist that these are the actual names.
Over on Tumblr, Ghirahim's fans refer to him as "Pete".
And there was prevalent overall usage of "Peppermint Kisses".
For one reason or another, it became common for the GameFAQs community to refer to Fi as "Steve" following her reveal in the teaser art from E3 2009. She is also known as "Zordiana" on Zelda Informer, to make fun of the people who believed that rumour.
Years ago, on some obscure Zelda fansite, there was a timeline theory which spoke of the origins of the Master Sword and claimed it was once a woman who became the sword. At the time it seemed a little weird, but no longer thanks to Fi's role as a feminine spirit residing within the Sword.
The Sheikah woman who helps Zelda is revealed to be named Impa. Also, Impa being the old lady confirmed a low-profile fan theory that the Sheikah have a roughly one-thousand-year lifespan.
Though she's not one of the main trio, there is indeed a fourth major goddess as was long speculated.
Keep Circulating the Tapes: A very unfortunate example with a patch of all things. The game itself, while likey technically falling under this, is nonetheless fairly easy to find. But due to the shutdown of the Wii Shop Channel in 2019, unless an Updated Re-release is made somewhere down the line, curious players who don't wish to resort to piracy may be left without it. Given this patch fixes a serious Game-Breaking Bug, this can be frustrating for some.
Original artwork shown at E3 2009 implied that this game would follow the same dark graphical style of Twilight Princess, if not even darker. This is part of what caused the shock/backlash at the cel-shaded style that appeared at E3 2010. Shigeru Miyamoto stated that the change was made because the dark graphics made it difficult to tell how enemies were holding their weapons, which detracted from the integral swordplay.
As late as Summer/Fall 2010, the team did not have any plans to include orchestrated music. This changed when Miyamoto told E3 journalists that orchestrated music was a must.
The Beetle was originally a rocket-propelled hand, but it was quickly found to not fit in with the setting (considering how much Anachronism Stew the series has already, that's saying a lot).
The original explanation for Link's Crimson Loftwing being so special was that it was the only kind of Loftwing that could travel between the sky and the surface. In the final version of the game, beacons of light enable access to the surface, and the Crimson Loftwing doesn't take Link directly there — he just drops Link to skydive into it.
The artbook Hyrule Historia, as well as one part of "The Making of The Legend of Zelda: Breath of the Wild", revealed that the sub-sections of the Surface were originally supposed to be connected with each other, but technical limitations made this a no-go, as they were pushing the single-layer disc limit already. A similar thing happened with Skyloft, which was much larger and multilayered in concept art. A good portion of the game's problems could be chalked up to technical limitations.
Miyamoto says the original Skyward Sword prototype that he played was more challenging than the final version. As he puts it, the developers were so used to the flow of the game that they made it harder for themselves, to the point that it would have been much harder for the average player. Thankfully for more experienced players, while the finished product was made to be easier, it was still more challenging than most Zelda games.