SPOILER WARNING! This is the entire text of the intro movie for "Wind Waker." Some of the questions you are asking are answered here. Others are answered in the game itself.
That said, Aonuma is absolutely correct. While some of the games appear to share a common timeline, there are only a few games where it is the same "Link" in each game. In fact, you'll notice that you get to choose the name of the hero in each game. "Link" is the name Nintendo has given the character to symbolize YOUR "link" to this world. The Legend of Zelda games are Action ROLE-PLAYING GAMES. You take on the role of Link. In fact, Wind Waker makes it very clear below that this Link is NOT "The Hero of Time" from Ocarina, although the two games share a timeline.
There is also the fact that the games rely a great deal on symbolism, and aren't necessarily meant to be taken literally. Without spoiling anything, there are changes in "Wind Waker" that would have been absolutely impossible to have come about in 100 years time. Yet, this is a FANTASY world, and our rules of time and space should not be applied to a world such as this. It's seems odd to me that people are trying to fit the games into a strict timeline, but are willing to forgive the fact that magic exists and things of that nature.
Please, just enjoy the games. How many Links there are and where each game fits in the "grand scheme" is pretty pointless. Just enjoy it and have fun. Because if you don't, some of the things that happen in Wind Waker will probably keep you up at night trying to piece it together even more.
Lastly, I'll also mention that there is an saying along the lines of "Those that do not learn from the past are doomed to repeat it ..." In the fantasy world, this tends to play out as a classic story that is repeated through time, and while the players and locales may change, the overall story remains the same, and so ...
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This is but one of the legends of which the people speak ...
Long ago, there existed a kingdom where a golden power lay hidden. It was a prosperous land blessed with green forests, tall mountains, and peace. But one day, a man of great evil found the golden power and took it for himself ...
With its strength at his command, he spread darkness across the kingdom. But the, when all hope had died, and the hour of doom seemed at hand ... a young boy clothed in greeen appeared as if from nowhere.
Wielding the blade of evil's bane, he seals the dark one away and gave the land light. This boy, who traveled through time to save the land, was known as the Hero of Time. The boy's tale was passed down through generations until it became legend ...
But then ... a day came when a fell wind began to blow across the kingdom. The great evil that all thought had been forever sealed away by the hero ... once again crept forth from the depths of the earth, eager to resume it's dark designs. The people believed that the Hero of Time would again return to save them.
... But the Hero did not appear.
Faced by an onslaught of evil, the people could do nothing but appeal to the gods. In their last hour, as doom drew nigh, they left their future in the hands of fate.
What became of that kingdom ...? None remain that know.
The memory of the kingdom vanished, but its legend survived on the wind's breath. On a certain island, it became customary to garb boys in green when they came of age. Clothed in the green of fields, they aspired to find heroic blades and cast down evil. The elders wished only for the youths to know courage like the heroes of legend ...