I've said this a lot, and I'll say it again.
I think that the best way to have a Zelda movie or Zelda series that's both good, and doesn't make the fans rage would be like this:
First off, animated. I think if it were animated in Wind Waker art, that's be amazing. Some type of cel-shading I think would fit really well.
Secondly, relatively silent with the speaking. Link barely talks in Zelda, and when he does, it's short things like "C'mon." If the movie were done with sort of a dark tone like Samurai Jack, I think that would work really well with Zelda, Link being mostly silent, and perhaps other characters would talk a little bit, but not so much so as not to draw attention to Link's silence. In Samurai Jack, early in the series I don't think spoke much. It was just him on an adventure fighting evil. If there was this kind of silence, more focus could be given on the soundtrack, which I think is an extremely important element to Zelda.
Third: I think Majora's Mask would be the best story. Relatively speaking, it's pretty short, compared to other Zelda stories, so you wouldn't have to cut out a lot to make it 2 hours and it's not just a hero's tale, but it takes on more emotional themes like loneliness and forgiveness (with the skull kid).
If not Majora's Mask as the story, I think a story involving Link and Tetra would be good. Tetra is a really entertaining character with a good personality, that definitely puts a twist on the typical Princess Zelda that's calm and well-tempered.