“I would change the Iron Boots from equipment to an item. If they could be turned on or off at the touch of a button, the Water Temple would be more fun. I wish I could travel back via time warp and fix that.” – Eiji Aonuma

This may be a good example of how good OOT was, the creator could not find anything major that he would like to change. If I remember correctly they did fix this problem in Twilight princess.