Ok here are some ideas for a cool Zelda game. Nintendo will probably never know about this, but there's dreaming.
I want an epic story. Look at this comic page:
The Hylians made these elite weapons a long time ago. You never hear that in the games. It's really much cooler to know this. -->
Have a cool background/history and TELL IT! Preferably by cut-scenes.
Use the retro aspects of the series in a cooler way
Imagine that at one point in the game you enter the Golden Realm. How about a movie with some cool voice saying the following verse:
In a realm beyond sight,
the sky shines gold not blue,
there the triforces might
makes mortal dreams come true
Real fans will go CRAZY over this. These are legendary and nostalgic things.
You add some more now. I'm thinking of stuff like gorgeous soundtracks (orchestrated music, like they make for the CDs!!) and more.