I've never wanted them to change the story telling of Zelda. They could probably update the technology a little, I suppose. I'd probably make a lot of changes in the gameplay, but Skyward Sword was a step in the direction I wanted it to go. Although, I'd like more of a Metal Gear Solid-style rewards system. By that I mean, accomplishing ridiculous tasks gives ridiculous rewards. So, as an example, if you go through the whole game without taking damage, then you get the Hylian Shield(Skyward Sword-style(Infinite Durability)) when you start the game. Something along those lines. Also, they could add the concept of enemies getting angry and trying to find you if they see a fellow enemy dead on the ground. Simple little adjustments like this could probably make a world of difference. I'd like to see some more mature story elements, I suppose. You know, real death. Not like in Twilight Princess where you thought Midna was killed. I'll be honest; I enjoyed seeing Ganondorf getting stabbed in the head and chest. He actually died. You truly saved Hyrule. That's not the same idea, though. They just need some people to die. I know it sounds kind of messed up to want to see more death, but it would allow for so much more character emotions and you would feel that much better when you killed the main evil character. Again, Skyward Sword took a step in this direction, where Demise almost killed Zelda. It felt more rewarding to kill him.
There's not much else I can say, really. I just want, an overall more mature Zelda game. I'm not talking about Twilight Princess and its T-rated...ness. Another way of putting it, I guess, would be to combine my two favorite game franchises. (If you didn't pick it up, those are Zelda and Metal Gear.)