Images from the original Japanese version showing things changed or removed in later versions.

Image total = 11

The Japanese version had three save files. But the Owl statues could not be used to create a temporary save.
The Japanese version doesn't show how many rupees or masks you have, but instead has a save counter (how many times you've played the song of Time).
A completly removed area. In the Japanese version you cannot get straight to the Bean seller by going through the right side of the Deku Palace gardens.
Instead you must go through the left side and enter a grotto hole there, which will take you to the place you see here. Go through this area and you end up in the second half of the right side of the Palace gardens.
This is where you come out.
Those strange Japanese eh? Instead of having 12 o'clock they have 0 o'clock.
Quite a different movie for when you first see Epona.
This puzzle involves freezing a flow of water to stop the turning wheel and allow you to get to the doorway into the next room. In the Japanese version the wheel stops moving a certain time after you freeze the water, meaning you have to time your shot to get the wheel to stop in the right position, this is very, very tedious. In later versions the wheel keeps turning until it is in the right position before stopping.
In the Japanese version, when you put on a transformation mask, Link will end up looking towards the camera. Although only a minor thing it does become quite annoying, in later versions Link ends up looking the way he was when the transformation started.