I'm confused. How was the story awful? It was the most developed and emotional story in franchise history. How were the characters meaningless? Characters haven't been more involved in a Zelda game since Majora's Mask. And how was nothing established? MotionPlus, the puzzle style overworld put to 3D (and perfected, at that), all items having equal use, and a freaking stamina gauge, which was a major factor to the gameplay. I don't like clashing with other people's opinions, but what you said couldn't have been more wrong.
Most of these are far from absolute statements, and I'd challenge you on most of these points. Vanitas didn't say anything "wrong", his opinion was just different.
I loved Skyward Sword, personally, but I think it's far from the franchise's best offering and certainly not one of the best games ever made. I'll admit to being very emotionally affected by some scenes, but overall I felt the story was mostly efficient - it got the job done and made you care enough to play through the game. I didn't feel a lot for the characters beyond Link and Zelda - everybody lauded Groose's story, and while humorous I felt that it was very rushed and poorly developed - to go from minor antagonist to sudden supporting protagonist as fast as he did is not particularly realistic. Vanitas never said that nothing was established in SS.
I tend to disagree with Vanitas' opinion overall because I very much enjoyed the game, but it's certainly not a wrong opinion.