It didn't fit into the Zelda series how so? Lemme: guess it's TOO different. Well, here's some food for thought: it's the SECOND game, so any change could have been put into the game. It could have been terrible! Most bashers on bash because they played other games before SS, so they go off to say, "How can this be a Zelda game?!"
Really, I challenge you to play the game. Use a walkthrough, if you must.