For those of you saying how "OoT had limited technology to work with back then, hardware was limited back then, and whatever other stuff back then" - why with all the justifications on a game's flaws? If that was the case, then why not compare ALttp to OoT, and say the same thing how ALttP was in 2D, it had limited technology to work with, and all the other justifications used to defend OoT? Cause with those kinds of arguments, that would mean you can never compare any Zelda game to each other, especially to previous titles, just because of different technologies used at the time. That would mean no Zelda game can ever be considered the best.
OoT was considered amazing because it was the first 3D game and that influenced the gameplay and introduced more of a story (although simple, but still a story!)- in other words, it improved on 2D zelda games (while building upon ALttP). Skyward Sword is revolutionary in that it introduced motion controls and changed the formula, added more depth to the stories and characters (which made people more emotional and even cry) - it took all the best parts of the series and introduced new elements, and it did that successfully.
If a game did something better and truly improved on many elements, it is the better game. Just as OoT improved on its previous 2D Zelda games, Skyward Sword improved on previous games before it as well. Constantly using the "technology was limited back then" is not a great way of arguing your case as the same can be said about OoT vs 2D Zelda games, when technology was even more limited.