Been a while since I thought up one of these, but been tossing around ideas. I just finished Majoras Mask for the first time and I'm working my way through Wind Waker now.
Basically to accomodate for it being a fan-game it'd have only two dungeons. Solves the problem of making an overwhelming fan-game project so many have.. I was thinking it would have a main town area somewhere, and focuses mostly on the problems of the people and the town itself. So though there'd only be two dungeons it would have many side quests for heart pieces, bottles, main items, mini dungeons, etc. Most of these side quests would start in the town, but have to be solved elsewhere.
More of an open world Zelda game would be good I think, and the player doesn't start off with some huge heroic task of saving the world or a Princess or anything, but instead just sets out to try and solve the main problem of the town... I had an interesting idea story-wise, that it could be something like a town with a crumbling economy and huge unemployment (America Town Hyrule?) or a drought, or some combination.
And so there could then be side quests to get economy booming in the town somehow, or find jobs for people, stuff like that. The two main dungeons would probably be part of a bigger quest. Whoever the antagonist is would be from a larger more prosperous town far away and the main dungeon would be there. They are planning on expanding their town, or building a resort maybe right where Link's town is, or a railroad that needs to go right through the tiny failing town... It's a cliche, but not one seen in Zelda really.
The idea of the two dungeons is that the player would progress back and forth between them, being able to complete only parts of it at a time based on whatever items you have at that point. And side quests are required sometimes to get items needed to get farther in a dungeon. The main dungeon could actually not just be in the prosperous town, but the dungeon could be the town itself. Mayor's Office being the central part, and walls all around the city. Citizenship required or you get attacked... Maybe some side quest to buy fake citizenship at some point, but usually just sneak into the dungeon through catacombs under the town. Just tossing around ideas at this point (and probably now way to ever make it, but still fun)
How's it sound?
And now for something completely different:
http://29.media.tumblr.com/tumblr_lqgen9M1FV1r1gpejo1_400.gif