I say they put in the scrapped dungeons and make it like a director's cut type game. And I don't think they would have to create the dungeons again, as I remember reading an article saying that the dungeons were made and put into the game, only to be scrapped near completion when the developers realized that made the game seem overbearing and long. (i'll try and refind the article that said this)
And made to make the triforce hunt not as annoying, instead of getting the charts then fishing for the pieces, have the locations that held the maps, (since Ghost Ship, fighting Iron Knuckles, etc.. was pretty entertaining and cool) but just cut out the middle man and have the direct reward be the triforce pieces.