Reading through this thread my response is an antithesis of sorts to JJ's original post. As a disclaimer, I'm not directly responding to anyone in this thread.
Twilight Princess showed that a game can feature many dungeons with each being unique and different from the last. The Forest Temple focused on turning bridges with the Gale Boomerang and using rescued monkeys to access new portions of the dungeon; Goron Mines is easily the most technologically advanced dungeon in the series with iron boot's magnetism coming into play; the Lakebed Temple is a traditional water dungeon; the Arbiter's Grounds is a plainer dungeon but made interesting use of rail elements; Snowpeak Ruins is a blend of overworld and dungeon with one of Zelda's deeper dungeon backstories; the Temple of Time is a rich throwback to Ocarina of Time with a cunning if misused item; the City in the Sky switched things up with an open top; the Palace of Twilight centered around dark magic and the Twili.
Majora's Mask succeeded with fewer dungeons because the three day cycle added an extra layer of tension to the experience and the transformation masks provided new gameplay possibilities. Whether hovering as a Deku, rolling around as a Goron, swimming as a Zora, or battling a boss as giant Link, I always felt like I was doing something different. Skyward Sword, on the other hand, offered a more mundane experience. Forest theme, fire, desert, technology, water themes? Been there, done that.
With a larger number of dungeons, there is a greater probability that Nintendo is compelled to experiment with new ideas due to the usual themes being drained up quickly. Twilight Princess is just one example. A Link to the Past has the most dungeons of any installment and I never felt I was retreading ground, constantly doing something new and admiring how much Nintendo could squeeze out of one SNES cartridge.