Ever since Fi was shown in the teaser art from E3 2009, It has been, for one reason or another, referred to as "Steve" in the GameFAQs community. It is also known as "Zordiana" on Zelda Informer to make fun of the people who believed that rumour.
Before Ghirahim's name was revealed, the GameFAQs community settled with Tracy, 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 has been an increased usage of "Peppermint Kisses".
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 that time, it seemed a little weird. Now, with Fi's role as a spirit within the Master Sword (though Fi has an Ambiguous Gender)...
Original artwork for the game, 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. Miyamoto has stated that the change was made because, when the graphics were dark, it was 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).
When the Crimson Loftwing was first introduced, they said that the reason it was so special was that it was the only kind of Loftwing that could travel between the sky and the surface. In the final version, it is a beacon of light that enables access to the surface, and the Crimson Loftwing doesn't even go to the surface, he just drops Link to skydive into it.
The artbook Hyrule Historia revealed that the sub-sections of the Surface were, in fact, 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 problems the game has could be chalked up to technical limitations, which is why people want the Wii U installment to correct said problems due to a greater memory.
Shigeru Miyamoto says that the prototype of the game that he played was originally more challenging than the retail version of the game. 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.