One interesting thing that I noticed about Majora's Mask, after thinking about it, is the way the owl statues address Link and his sword. They have this phrase engrained in stone:
Ye who hold the sacred sword, leave proof of our encounter.
Referring to the Kokiri Sword and its upgraded forms. I just thought that it was extremely interesting that the Kokiri Sword is considered "sacred" in Majora's Mask. There are only a few items considered sacred in its prequel, OoT. Those items are the Master Sword, the Hover Boots, and the Triforce. Nowhere in the game's text does it refer to the Kokiri Sword as being a sacred object.
Another interesting thing is the design of the Kokiri Sword between the games:
The differences almost make them look like
two different swords. The differences could possibly make up for the differences in "sacredness." Also interesting to note that the one from OoT has a crystal in it, much like the Master Sword and the Gale Boomerang, which we know to contain spirits.
Also, up-grading swords is not unique to Majora's Mask. In A Link to the Past (the game I think a lot of Skyward Sword's story will revolve around) you got to upgrade the Master Sword twice. Both of the upgrades still allowed the Master Sword to contain the power to repel evil, the obvious proof are the sword beams as no other sword, except for the Four Sword (when powered to repel evil), have beams. So, the sword still contained the spirit of the Master Sword. If the Kokiri Sword is indeed sacred, then it might contain a spirit as well.
The only flaw that I see, besides our lack of knowledge of Skyward Sword, is the fact that the Gilded Sword is an upgraded version of the Kokiri Sword where the upgrading of the sword took place within a game dated long after Skyward Sword. However, an explanation of this could be that the Gilded Sword was modeled after the sword that our new character takes on. Its a probable theory that could explain it, but until we get more information from Nintendo, or Skyward Sword, we cannot be certain.