Besides obvious technical advancements, I personally think that 3D Zelda's have gotten worse since Ocarina of Time was released. While I deem Majora's Mask to be on equal ground; Wind Waker, Phantom Hourglass, and Twilight Princess all lack in certain areas that prevent them from being a complete experience, and certain design choices make them less memorable, and less engaging than their N64 counterparts.
For what it's worth, though, I do agree that Link's Awakening was the best 2D Zelda, narrowly edging out A Link to the Past.