The hardest part of the Water Temple is that one of the keys is hidden way better than the others, and if you start opening doors in the wrong direction you will run out of keys without it. Combine that with the clunkiness of swapping to/from the Iron Boots and raising/lowering the water level, and the place quickly grew tedious and frustrating.
The 3DS remake added an extra camera sweep and some decor highlighting the hidden passage where that key is found.