The reason I think Super Metroid is fantastic is the openness of the 2D world, and the subtle details in the game to give it character and atmosphere.
Super Metroid is full of small details that when you see them give you goosebumps. The world is gigantic and I have had truly emotional moments in that game which basically has no story, which proves that they succeeded in the atmosphere.
And this isn't nostalgia talking I didn't play the game when it first came out...but truly experienced first and beat it as a virtual console game.
Super Metroid was the perfect difficult, a truly amazing world, and a game that never forgets you are playing a game...but succeeds in being more than a game. Only two other 2D games are truly as special as Super Metroid and those are Zelda: Link to the Past, and Super Mario World 2: Yoshi's Island.