**Last updated February 16, 2015**
Some new info on how Nintendo remade the boss fights in Majora's Mask 3D, courtesy of "Iwata Asks." I bolded the salient parts.
Yamamura: So, instead of giving out or forcing the answers onto the players, we focused our energy on how well we can communicate the meanings of the missions to the players. By doing this, I think we were able to make the challenges more comprehendible while keeping the same level of challenge as the Nintendo 64 version.
Aonuma: A great example for this are the boss battles.
Ooiwa: That's right; Aonuma-san said that he wanted to change all of the boss battles.
Aonuma: I've been saying that all of the boss battles are weird. All of them. When you first face a boss, it is natural to start looking for its weakness so you can figure out where to attack it. However, in the Nintendo 64 version of this game, you couldn't see the weaknesses at all.
Iwata: This is because you created this game as a challenge for the users to figure it out themselves, right?
Aonuma: This would be all right if the users understood this while they were fighting. However, this turned into a game where players won by randomly attacking the boss, without really figuring out what was its weakness.
Ooiwa: I personally wanted to fix this too. After I found out we had the same concerns, we reconstructed the battles by focusing on making the objective easier to understand, ensuring that there is the "a-ha" moment for the players, and the strategic elements that are needed to take them down wherever possible.
Iwata: So, you've remade every single boss fight?
Aonuma: Every single one of them. However, their models are virtually the same as the Nintendo 64 version.
Yamamura: However, the bosses' movements and strategies to take them down have all changed, so it took about the same effort as creating the stages from scratch.
Iwata: Well you say that quite frankly, even though this is supposed to be a remake.
Yamamura: (Laughs) We put in that much effort in creating this game, so it should be more convenient to play for players that are new to this game. It should also be refreshing to play for those that have played the Nintendo 64 version.