Let me preface this by saying that the game is fantastic and one of my favorite games of all time.
But, the one problem I have with the game is that it is too easy. I understand that having played Zelda games all my life, I've probably seen most of the tricks they can pull to make dungeons challenging. And sure, I can intentionally restrict myself in some ways to create further difficulty. All of that is well and good, and is why I still enjoy the game. BUT - I feel that they could have made the dungeons far more tricky, and far more clever. There are a score of items that we get in one temple, and use very rarely in future ones. This is where they missed their opportunity. Whenever I want to give an example of a perfect dungeon, I point everytime to the Stone Tower Temple in Majora's Mask. It is the culmination of everything that the player gains throughout the course of the game, and the puzzles require the use of each one. One must be able to use the Goron Mask, the Zora Mask and the Deku Mask with incredible finesse and precision in order to complete the temple. On top of that, it requires a great deal of control over Link's human form and the items that he can use, limited to the Mirror Shield, Hookshot, and Bow though that may be. The temple as such is very challenging and quite cleverly designed because it uses everything that Link has at his disposal in tandem. This is where Twilight Princess COULD have shined - imagine a single puzzle that requires the use of the Spinner, the Ball and Chain, the Double Clawshot, the Dominion Rod, the Bow, the Iron Boots - all of these items that Link acquires throughout the fairly lengthy game. It would be one of the most revered and well known puzzles in Zelda history, and would have made the game far more difficult and suitably challenging.
The game is great, but could have been even greater had Nintendo taken chances with their dungeon design and made some devious, clever puzzles.