SOTN wins pretty decisively.
SOTN has the better soundtrack, bigger map (x2), much more variety in gameplay, deeper character advancement, more utility/traversal abilities, and a ton more goofy stuff just for fun (brass knuckles, shield rod, etc).
I mean, going head to head, where does Super Metroid actually win? You can argue Metroid has the better soundtrack, it doesn't but it is worthy of debate. Graphics, story, combat, SOTN wins. I guess if you really enjoy the "platforming as a puzzle" aspect of these types of games, Metroid has a lot more areas that are purely platforming.