I kind of like these ideas... I was thinking for a water temple, there could a way to change the state of the water. For example, you could press a switch and all the water would evaporate, moving it out of the way but making high up doors unreachable. Some could turn the temple to ice, creating stairs, platforms, and other things of ice but blocking off some areas. And of course, a switch for regular water.

Customizing Link could be a good idea, but as long as he remained largely the same. Just a few small changes, like maybe his tunic style, would be enough. I think TP length, maybe a bit longer, would be good for the main quest, but there should be more sidequests to add to the game. They shouldn't all be collecting quests either; MM style ones would be cool. I'm not sure what you mean by multiple playthroughs, but it would be nice to be able to do some dungeons out of order. I think a giant bird would be pretty cool; a way to move around quickly. If there was anotehr sky temple, maybe the boss fight could be against a winged creature from atop your bird, and the arena could be the airspace around the temple. The temple could also be burning or something to add to the atmosphere.