I would love a dungeon were you are in skyloft. (Not on skyloft, inside of its clouds.) And you are attempting to exit it, but you fall back into hyrule. Then you must convert water into new clouds to make yourself back into the clouds.
And for my second idea, is for OoT3DS. An new optional dungeon that uses my idea kind of gimmikly. Since there is extra debpt possibilities. X-axis, Y-axis, Z axis, and the non-existant W-axis that can really test your mind. By turning off and off the w-axis from going to different part of the temple, the temple's objects and items look different and odd. But by obtaining and useing the trinity of trut, the w-axis in that temple will be completly restored. Kind of confusing to understand when explained.