Super Metroid may well be the best Metroid game. A Link to the Past, while decent, isn't nearly the best Zelda game.
Frankly, Super Metroid just has better action, better atmosphere, arguably better music, and smoother controls. It has a flow to it that A Link to the Past lacks. The world is interesting and fully-realized, with a real sense of history and connection between each area. The action is absolutely perfect--it's an ideal platformer, shooter, and adventure game, and excells in all those departments. Samus is a compelling protagonist, perfect for this type of game and every bit as dynamic and adaptable as she is in any of the other Metroid titles.
A Link to the Past, while it offers decent gameplay, is so utterly drab in the visual department that it's distracting, but on top of that, neither Hyrule nor the Dark World ever struck me as all that interesting, seriously inhibiting the exploration element. It gets props for tightly-packed secrets, though, and lots of them; you'll feel compelled to explore even more than you might in Super Metroid, because it at least feels like multiple rewards are on every screen. Unfortunately, the game really is overcrowded with items, and item-switching is never easy in Zelda games. Here, it just feels like too much--I think the original Legend of Zelda struck a much better balance, and Link's Awakening used items more interestingly.
I know this isn't a popular opinion on this site, but A Link to the Past is overrated. Super Metroid, while perhaps somewhat overrated, is still a fantastic game. While both paved the way for future entries, Super Metroid is arguably the pinnacle of its franchise while Zelda had much farther to go.