I always wondered why in all the 3d Zelda games they never had the really awesome feature were when you health is full, you shot little beams out of your sword. I would of LOVED for that to be in OoT especially.
As for an item, I'd say Rocs feather. I always wanted to jump in a 3d zelda game... if Zelda had some platformer elements to it, it would be very very awesome, but that would make it too much like Mario.