The story might be important, but if I wanted to read a good story, I'll go read The Sound and the Fury again. But unless I can start making Benji and Quintin fight moblins and collect rupees to buy flippers from the king of the zoras, books and video games aren't the same thing.
Do you really need a good story to play a video game? I don't think I've ever said "I'm sorry Link, I can't guide you through the great palace to beat your shadow because this story makes absolutely no fucking sense. I have no motiviation."
And even if the story is just being rehashed over and over again, all the Zelda games with essentially the same plot (The original one, A Link to the Past, Ocarina of Time, Wind Waker) are so fundamentally different that it's not like playing the same game over and over.
And is it really that bad if Nintendo just keeps using the same characters, i.e. Link and Mario? The last original idea Nintendo ever had was Pokemon, which was a gay-up. I'd rather be the same fairy fag over and over again than trust Nintendo to try and create a new hero, which would end up being something even faggier than link.
And it's not like Nintendo's lack of creativity is even close to being as bad as Square and the Final Fantasy series. Saying Final Fantasy 8 was a sequel to Final Fantasy 4 is like saying Disney's Aladdin was a sequel to Disney's The Little Mermaid.
In short, the story isn't nearly as important as how fun the game is.