It seems to be a definite theme of Zelda games that the initial temples come as a set of three: earth, fire, and water; and that the water one is a significant difficulty jump from the previous two. The true water temple also tends to require you to think along another dimension - in Ocarina of Time it was a true three-dimensional dungeon that shifted (moving the water level not only changed which areas were accessible, but also changed how several rooms behaved). Twilight Princess instead based a lot of the temple around shifting the flow of water, with a room containing a 3D maze thrown in for good measure.
In Skyward Sword the third "temple" is actually the Lanayru Mining Facility which is more of a sand temple, but it still has the difficulty jump. Except this time it's caused by the timeshift stones, which gives alternate versions of a lot of the rooms. I've still not quite got my head round how the stones are supposed to work, as they give a window into the past yet manipulating things inside the past area can affect in real time things outside. Like turning a fan inside a zone, which moves (as you turn the fan) a barrier outside.
Then again, Zelda games are no stranger to messing with time - take the time travel from Ocarina of Time, or the season changing from Oracle of Seasons.
The other odd thing about it is the music. Like with Skyview Temple it reminds me strongly of previous Zelda games, except this time I can't quite place the music from it. Something about it sounds a bit like the theme from the crypt in Minish Cap, with maybe a bit of the Temple of Time theme thrown in? It's not as clear a reference as Skyview Temple was. Any thoughts from other Zelda players?