About Skyward Sword, yes, it's hated because of the Zelda cycle... and because it was very different in world structure and level design and exploration, etc. to a point where people didn't like it because it wasn't like any other Zelda game. Which is stupid because it still felt like Zelda and it was the best one at that.
Anyways, how the hell to you define "most popular"? Do you say that because looking around the internet you see everyone loves it and what not? I've got a better solution: numbers. And this "one of the top 3 most popular" Zelda game is actually the worst selling home console entry in the franchise and by quite some margin. And that's considering it came out at the peak of the franchise's popularity.
I'd argue that it's "hated" because it's simply not good. What it does have is a lot of fan-service, a unique art-style, and superficially interesting combat mechanics.
I believe in honesty, civility, generosity, practicality, and impartiality.