Disclaimer: I don't own Zelda or the characters Nintendo only the plots. But obviously you can write these.
Author's notes: Okay, I love the loz, but I've found that I can never finish a Zelda fanfic. So here are some ideas I came up with that might give you some ideas for your own stories or if you just want to like one of these. (It's okay really).
The Gerudo Prince
Oot
Plot
Instead of Link's mother bringing him to Kokiri forest and him raised by the Deku Tree. He's picked up by the Gerudo and raised as one of their own. Since he's a male, but not a true Gerudo, he gains the title (that's not his true title) The Gerudo Prince. Link is a high ranking general who commands an entire legion that would follow him to the death. He travels to Hyrule with Ganon and meets the beautiful princess Zelda, or Malone exedra (which ever you want) (as an adult) and falls deeply in love.
When he learns of Ganon's plot to attack Hyrule he makes plans to stop it. Meanwhile Ganon, not knowing about Link's plan, attempts to have Link killed, fearing that he might pose a threat to his throne. Link manages to escape and joins the Hyrule army with his faithful troops (maybe already during the battle), and that's all the plot ideas I think I should give for this plot.
Characters
Link
His strength is has increased tenfold, as has his skill with riding and archery. Eg, he once challenged a man, with the golden gauntlets, at a strength contest and won, more knowledge about magic but less skill with it. Darker skin, wears black tunic, black Gerudo pants, black gloves, shin high black boots, and a black head band. (Guess he likes black).
Zelda
Very little change or change as you will.
Ganondorf
Once thought of Link as a son, change at will.
Nabooru
Link's second in command and she respects him more than Ganon himself, change at will.
Hope this helps you. If you do write one of these as a result of me please comment me so I can read it. Expect more.