Images from the "A - B reversed" development period.

Image Total = 39

This was pretty much the final game, the control style is the same as the final one except that the 'A' and 'B' buttons have switched roles.

Although quite a lot of stuff was still being changed it was mostly minor, the story had been finalised and most things were probably just being tested to make sure they worked properly.

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Learning the Bolero. Although I should imagine the text is similar, if not the same as that in the final version, a translation would be nice.
The little arrows and squares at the bottom of the text boxes are bright green, obviously because the 'next' button is the B button, which is green (whereas final version has blue boxes/arrows, and uses the blue A button).
Here's a good shot of Sheik's blue eyes. In the final version Sheik's eyes are red (all Sheikah have red eyes apparently), this was probably done to make Zelda and Sheik seem more different (Zelda has blue eyes see).
This one is odd, Sheik meeting Link on the warp pad in the Death Mountain crater. What makes it even weirder is that Link has the Ocarina in his hand, which means he has just played a song, and the only song you play in the crater during a cinema is the Bolero of Fire.
The only really good explanation for this is (as some kind person pointed out) that originally you may have had to walk onto the warp pad in an area to activate the song learning, now the problem with this obviously is that it would be easy to miss getting a song, which would be why it was changed. Although how you would have gotten to the warp pad in the Graveyard remains a mystery, maybe the Bean Platform there originally went further than it does now.
A rope bridge leading down from the ceiling to the floor, the quality (or lack of) of the screenshots means I can't give an accurate guess as to where exactly this is.
An aggressive Deku Baba, the ones here in the final version just rotate around in circles.
Yellow-blue flames, final version has red-orange.
The camera angle here seems ever so slightly different from the final one (picky, I know :P).
Yellow-green flames now.
A cinematic start to the archery course, final version just has the camera follow you like it normally would when you're on Epona.
Exactly how Link has the bow out without the camera going into first person view or behind him I don't know.
Adult Link with the Magic Beans equipped, a final version impossibility.
Also the wooden bridge supports have little angled supports of their own, not featured in the final version.
Very different, a tent on each side of the bridge, crates, a worn path and the bridge is different. I believe this is a scan from an old N64 mag, if anyone could get a higher quality picture..?
The Great Fairy of magic giving Link magic power, this Fairy appeared in the OoT movie trailer but for some reason between then and the game's release was replaced with the scantily clad thing we get.
I think I prefer the final version Fairy, this Fairy has no facial features, and looks, well... ...weird.