I've heard a few theories on how the different games fit in chronologically. But most of them assert that while some of them share a Link (like the Oracle games or the first two ever), it's nonetheless a number of different Links in each era. My guess is that at the end of Skyward Sword, it'll turn out that Link and Zelda have left an inexplicable genetic constant on the whole of the Hylian race that keeps reincarnating them.
Or hell, maybe Link is a kind of Time Lord, and his regenerations end up making him exactly the same each time but with no memory.