My advice is, don't try for a 2d remake of any 3d Zelda game. It's one of those cool idea's that would be impressive to see, but it would take too much time and effort to make it a reality as opposed to making a new Zelda game of your own. Also, you won't have as many limits if you're making your own game.
And something I think you should use in the story... The Lost Woods, they are mysterious, magical... within the woods are many paths that lead to many places... oooo, just think what you could do with that huh? Maybe Link could stumble on to a new land through the Lost Woods? You could use the Lost Woods as a sort of gateway to go to many different lands. Maybe Link would have to follow certain secret paths, and maybe he could find scrolls or something that reveal new secret paths to him, leading him to discover new lands or secret groves. The Lost Woods definitely has possibilities to play a main role if you want it to.
EDIT:
Btw, I haven't forgotten about getting those sprites for you. Life just got a little crazy there for a while. I'm still working on some sprites for Martijn, but lately I've been making rapid progress on them, so I should be starting on yours soon if all goes well. I just wanted to let you know.
EDIT x 2 (Oh my!):
Hey Cypras, I just realized that you already have Link walking with a charged sword, he just walks in place. So you've already got the correct sprites, I even checked them in the MC game. The sword doesn't flash like in the MC game, but you could do sparkles or something. It's not like it has to be exactly like the MC style. Anyway, so all I need to do is get the sprites of Link walking with the bow pulled back, which should be simple. ^_^
Also, how is the game coming along? There haven't been any updates for a little while, so I'm just wondering.