Here's my little opinion on this, but remember, its only my opinion, I don't know for sure
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****** MINOR SPOILER ALERT FOR OoT (if anyone cares) **********
If you go back to the original Legend of Zelda game (for NES), it was a story (read: "legend") about the Princess Zelda. All the games since then have primary focused somewhat on the tale of Zelda, even though you play as Link. Think about it for a second, using OoT as the prime example. Without Zelda, there would be no legend. While Link is a very important role in the game, Zelda its just as important if not more since she is one of the Sages and has a piece of the Triforce, just like Link and Ganon. So in that sense, the game could have been titled the Legend of Link or the Legend of Ganon, since all three are the primary (perhaps secondary) characters in most, if not all the games. In the words of my college english class, the three of them (Zelda, Link, and Ganon) form an exotic Gothic Triangle. The two empowered males (assuming you can consider Ganon "male" =p) fight for control of the endangered female, perhaps with some love interests. OoT really complicated this, but I think it fits. I think Wind Waker will cement this "gothic triangle" argument for you once you play through it. I have already played through the first (short) half, and can already see that it fits quite nicely.
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Anyway, if I confused you as much as I confused myself, let me know, and I'll try to clarify my thinking on this.