I "admired" the dungeon naming scheme. The Fire Temple was the Earth Temple *snicker*. The Skyview Temple, despite hardly any proper view of the sky, subbed as the Forest Temple. xD
One thing I loved this time around was the dungeon key bit. Just a fun, final puzzle. And I thought Klok...kalok...Koloktos[?] was the best boss the series has seen in a while. Design was amazing ('spesh when he is holding all 6 swords up), he was pretty tough, and can be taken out in an extremely unique way (not with the master sword, but with... his... D: ). And I did think the Ancient Cistern was one of the coolest looking dungeons in a long time.
(Hey, look, Aeolous, I'm complimenting!)