Cancellation: In Japan, the GameCube version of the game was canceled...for on-the-shelf retail, at least. It was officially sold via Nintendo's online store, although rumor has it that Nintendo almost entirely canceled it like other late GameCube titles that were converted for Wii release such as Super Paper Mario. The Wii Uremake is based more closely on the GameCube version, making it the first time it'll be sold new at Japanese retailers.
Zelda Director Eiji Aonuma feels he did not make Twilight Princess as epic and grand a game as he intended. He said that he regrets making Hyrule a realistic, grand size, saying that with that size, they were unable to fully take advantage of the space that they created. He had said he planned to use that grand scale as a starting point in the development of Skyward Sword.
Fan Nickname: So, this Link is the "Hero of Twilight/the Gods/Light," right? He must be, because three of the numerous other Links throughout the series had similar titlesnote He's referred to as the "Blue-Eyed Beast" in-game, but that hasn't really caught on because it's specific to his wolf form.
It was heavily suspected by most fans that the Hero's Shade is actually the Hero of Time, due to strong yet cryptic in-game hints and the series manualHyrule Historia eventually confirmed that. The other theory that TP Link is his descendant was also confirmed.
After the game was shown at E3 in 2005, a letter in Nintendo Power Magazine issue 195, asked if Midna was the game's titular Twilight Princess. Nintendo Power said in response that the developers aren't saying anything so that they wouldn't spoil anything for the audience. Later, after the game was finally released, Midna turned out to actually be the Twilight Princess
Shrug of God: Even Eiji Aonuma himself doesn't know the meaning of Zant's scene at the end of the game, as the leader of the team that created the cutscenes was known for being a bit of a lonewolf. Nevertheless, he had immense faith in him and didn't say anything about the scene itself, even though he didn't understand it.
Koji Kondo planned on there being more music done with a live orchestra, presumably the same amount that Super Mario Galaxy ended up having. He had to put such plans aside because he ran into problems with Variable Mix among other things.
There was also originally going to be a magic meter, as can be seen on the Wii version's box. Unused text suggests that magic would be required to transform back and forth.
On a possibly related note, green Chu jelly can accidentally be created in the Wii version. It is useless in the game, and has no item description nor Item Get! text, suggesting it's a leftover from earlier builds that did feature a magic meter. Green Chu jelly does return in HD, except this time more as an artifact and Development Gag, as its flavor text directly acknowledges the item's lack of use.
The companion game, Link's Crossbow Training, was meant to be a direct sequel akin to Majora's Mask. However, production would have taken too long, so it was decided to be a simple spin-off to take advantage of the Wii Zapper.
A minor example since it might not have played any major part in the game, but Link was originally going to be able to ride the goats he herds. Word of God is that, while not an implemented feature, Link does still know how to do this in-canon.
The trailer shows Link battling what appears to be a Moblin enemy that carries a large hammer, but it does not appear in the final game.