The first 64-bit version of Zelda, was originally conceived as a way designed to use the features of 64DD. Internal Clock, rewritable discs with a size double what had ever been used on the cartridge, internet connection and tools for editing images, Zelda 64 was presented by Nintendo itself as a title so huge that it would be impossible to implement on a normal N64.
All this because of the possibility of 64 Disc Drive. But there was only one small problem: the 64DD was not greeted with much interest from professionals, remembering the bad purpose made by all previous add-on for console, the DD was growing slowly postponed, Nintendo itself lost confidence in the project and it was not clear if it ever really left. At this point, Nintendo had no other choice, because of low sales of the N64, they announced that Zelda 64 would have been ported to normal cartridges, so hoping to renew interest in the console market. But this change meant they had to remove all those interesting features that would have been only possible thanks to 64DD and part of the game and history had to undergo an extream cut.
From an interview with N-ZONE magazine (translated with google and reported by GoNintendo) we can read that Aonuma admits that Ocarina of Time originally had more temples and magic abilities that were cut.
Eiji Aonuma: Yes, you may be absolutely right, although I can not remember exactly all the details. There really is a difference between the temples, which we wanted to integrate and those that exist in the final game. And that had something to do with magic. We thought of integrating some actions, some plot threads, and some puzzles that have something to do with magic abilities.
We have come to the conclusion that other, already existing, just regular items to be a worthy replacement. So we had originally three temples, which would capture the young Link, three temples for the adult Link and three in which he was to learn each spell – but instead we have eliminated a temple of it. In the final game is now so 3 plus 3 plus 2, or 8 temples to find.
Also, some more interesting info from the early beta / prototype version of Zelda 64 were shared in the Iwata Asks dedicated to the Ocarina of Time 3D remake:
Iwata: Oh, he wanted to make an FPS (first-person shooter).
Koizumi: Right. In the beginning, he had the image that you are at first walking around in first-person, and when an enemy appeared, the screen would switch, Link would appear, and the battle would unfold from a side perspective.
Iwawaki: But…I do think we tried out a first-person perspective a little.
Osawa: I think we made something to try it out, but decided it wasn’t interesting visually and abandoned it right away.
Iwata: You were originally developing The Legend of Zelda: Ocarina of Time for the Nintendo 64DD.13
Koizuma: Yes. Miyamoto-san said he had some ideas, like leaving behind all of Link’s footprints.
Iwata: Yeah. (laughs)
Koizuma: That’s why he started saying that if Link was going to ride a horse, he wanted to include mounted archery and one-on-one battle. (laughs) We were able to include the mounted archery, but not the one-on-one battle.
Iwata: But later you included it in The Legend of Zelda: Twilight Princess.
For more info read this article: Project Zelda 3D – The Development of Zelda 64
Thanks to Superfun64, 8PM and thedragoonknight for the contribution!
You can find more info about Zelda: Ocarina Of Time in the Zelda Wiki!