Super Metroid is great and genre-defining and an all-time classic and all that, but it kind of sucks to play. Samus' huge sprite and big, floaty jumps, combined with the lightning-quick enemies and the inaccessibility of missiles, mean that "optimal" play is just running through corridors while spamming your blaster and tanking hits.
On the other hand, it probably has the best sense of exploration and discovery in the series, which Fusion and Samus Returns lack due to their linearity and more predictable structure. So in the end, I guess I have to give it to Zero Mission? Zero Mission does everything really well, even if it isn't necessarily the best at any individual element. I haven't replayed it in forever though, and I don't even think I have a legal way to do so anymore. C'mon Nintendo give us GBA VC on the Switch already, yeesh.
In any case the actual best Metroid is Prime 2.