I adore Ocarina of Time, but I dislike that it became the standard 'framework' that the rest of the series had to follow. This is a problem for the Zelda franchise in general, and to some extent Nintendo as a whole. A lack of innovation I suppose. 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 would say that A Link to the Past is what set the framework. It was the first game we had with multiple worlds that you'd travel between, which were unlocked after the early set of dungeons. It also introduced most of the equipment that we associate with Zelda. The Hookshot, Link clearly has an Ocarina, which I cannot spell, bottles, catching faeries in the bottles, ect. Don't overlook it because of the graphics. The Gameplay was set there. Ocarina of Time was the 3D graphics implementation of the exact same structure used in ALttP. Plus it was the backstory of ALttP.
Yes, I know all the zelda historia stuff, but it is. As for the little differences, they don't bother me. It lines up enough. Thats also one of the reasons I loved Wind Waker more than most people seemed to. It was a proper sequel to OoT.
Man, I like the less popular ones, don't I? Zelda II, Wind Waker...