Oh, goodness, it's a shame I didn't notice this earlier. I would have loved to have been a part of the discussion.
If you need any assistance, I'd be glad to help in any way I can. I'm afraid I have very little experience in programming; most of my skills are common and people have already stepped up for their relevant jobs, so I'm just kind of here as backup. I have a passion for writing and would love to be a write or editor of sorts. (There are far, far too many fan games out there with dreadful grammar.... Of course, seeing experienced people like Shadsie volunteering as writer makes me think I really shouldn't be concerned. XD) I wish I could help out with the music, because I love that kind of thing, but I don't really have a proper method of recording and no actual music programs with which to make digital music.
I love the ideas discussed so far. I wasn't sure of Dragoncat's idea at first, but after reading through some of the comments and revisions others have discussed, I actually think it sounds really neat. I also liked ihateGhirahim's if there's some way to combine them.
Oh, however... I personally am not a huge fan of Fletcher being SS Link and Zelda's son. It's just kind of a thing with me that I don't like the idea of their children being characters in fanfics and stuff that I read. Just throwing it out there; if everyone else agrees to it, then who am I to tell you what to do? XD I'd be okay if they were ancestors or grandparents or something, but your idea takes place too soon after SS to do that. It just seems so... cliché. And what would have happened to SS Link and Zelda if they're no longer there? Or is Fletcher older? (...If this has already been discussed, I apologize, because I kind of skimmed some of the later posts.)
And yes, a female villain would be fabulous. Magic is a must, too. Is there going to be an instrument of some sort? I absolutely love musical instruments in Zelda games, so I'd love to see one, even if it's just a side thing, haha.
Either way, whether you need my help or not, good luck, everyone. ^^