From 1987 up to present we have seen Link change from dark hair and dark eyes, to blonde hair and blue eyes, then back to darker eyes just in appearance. There are different Links somewhere. I knew when I first saw OoT before anyone knew it's true connection in the series. Totally different looking character.
His shield has transformed from a cross being the center graphic on his shield, to the Hyrulian crest from OoT.
Ganon became known as Ganondorf, Prince of Thieves in Zelda: a Link to the Past. And was first seen in human form in OoT. Instead of being a pig-like creature that could be destroyed by well aimed silver arrows in the original.
It's just very confusing to sit down and think about which Link is which. I'm positive a guy like Miyamoto plans to connect all of the Zelda franchise together one day.
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First Generation Link starred in OoT, and MM. But also had roles in the SSB series. He must be the same Link that was found in LttP, because that's when he met the King of Hyrule, right?
Second Generation Link is the WW Link, I think, and went on to star in Link's Awakening. Upcoming game inbetween somewhere, maybe?
Third Generation started it all with LoZ and Zelda II: the Adventure of Link.
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That is how I THINK the story fits together so far.