That's actually what happened with every single Zelda game to date after Ocarina of Time. Because it's new, and has the title "The Legend of Zelda", everyone expects it to be the best ever, flawless. Take a look at Twilight Princess. On first reaction, ZOMG HE'S A WOLF!!EON111!!, but as you get deeper into the game, you realize that Hyrule Field is too barren, that the game is too bland...then you get into the more critical flaws of the game. Same thing with Skyward Sword - because it's new and has the title "Legend of Zelda", it's automatically the best thing ever. I do agree that the art style is the best thus far, and the gameplay is the best thus far, but everyone is heralding it as the best ever without looking at anything other than art and gameplay. The story I found was particularly weak. It ended EXACTLY how Twilight Princess ended, which was weak in my opinion. The characters were incredibly unimportant save a few, just like Twilight Princess. Overall, SS is just TP version 2.
Anyway, SS missed out on quite a bit that it should've had. The first playthrough is mindbombing awesome, but subsequent playthroughs really make you think about it. Anyone who has just 100 percented the game will say it's the best. But anyone who continues to play the game will see that characters were particularly flawed and useless, that areas truly were barren, and the game could've used a lot more challenge among other things.