While Wind Waker, Twilight Princess and Skyward Sword (to a lesser extent) each had their own added mechanics, it is clear that they borrowed heavily from OoT. In my opinion all three do what Ocarina did, but better. I mean, going purely off of nostalgia sure OoT is the best, and from an innovation standpoint as well, but the refinement found in the later console releases trumps OoT, and gameplay is one of (if not) the most important aspects of a game.
I like it when franchises are willing to experiment and change the formula both in story and in gameplay. That's why Majora's Mask is my favorite, and that is why I love almost all of the handheld titles and hold Links Awakening, Oracle of Ages, and Spirit Tracks in very high regard.
As a sidenote, I love Skyward Sword and everything new that it brought, but I hate motion controls because they are often too hard for me (being physically disabled). This is why I don't hold it in such high regard specifically.