(For the short version, skip down to the second to last paragraph)
I remember the Temple of Ancients... here's my view on this.
Dungeon seems unique, but cliche. The whole clock and Zodiac thing is perfect as is. However, my problem comes with floor 3. Mini dungeons of each dungeon is lame in itself as an idea. What gets worse than that is having to refight bosses that you already beat right before you... fight a boss. Which likely has multiple forms. This has been seen in too many Zelda games and non Zelda games.
Example of mini dungeons...
Majora's Mask (moon children)
OoT (Ganon's Castle)
Wind Waker (Ganon's Castle) even had the boss refights.
Examples of Boss refights...
Twilight princess (Zant)
WW (ganon's stuff)
Example of multi form bosses...
Just kidding, all but Skyward sword pretty much did that.
What I'm getting at is try something less cliche, no one likes to fight all the bosses that they beat ages ago. If I were you I would do something that involves mastery of your items.
For instance, a series of rooms that requires you to use a single item to progress to the next one. Whether it's a matter of skill or timing I dunno, but it would be something fresh for Zelda. Use dungeon items in an entirely new setting. Testing your memory instead of cloning a past experience. If combat is a serious must, then each room could have a miniboss corresponding to a specific item as well.