I'm open to assist with anything that's chosen. However, if I had to weigh the options, here's what my report would look like:
Ocarina of Time 2D
Already in the works, and looking good.
Majora's Mask 2D
This game would be ok to make as long as we plan well enough for it. It would be easy to recreate the world in MC style, with some obvious edits concering velocity and 3D aspects.
Wind Waker 2D
This would be very hard to do, since a lot of the game was made for a 3D environment. Also, in 2D, it would look very bland. Think of the great sea. Most of the map would be just water.
Oracle of Seasons and Ages
This is another fairly simple option. The only difficult parts would be the password system and ring system. The password system might be able to be substituted by just making the two Game Maker exe files "read" from eachother.
Thematic Engine
By far the easiest thing to do, but it might get boring if there wasn't a game to go with it.
Original Game
This would be difficult to set up and work on properly unless everyone can cooperate, but it would give more freedom of development. I'm okay with this as long as the story doesn't go out of proportion.