"Super Metroid" to me is the second best Metroid, and original "Metroid" is the best.
I hated all the handheld Metroids I played. "Fusion" was distressingly linear, "Zero Mission" was a huge disappointment (I was expecting "Metroid" to be retooled into a GBA "Super") and "Metroid II" was the same caverns and textures over and over with a descending lava lake that existed to limit exploration until a section was cleared.
On the other hand, I played an extensive amount of "Super Metroid" before I ever touched any of the previous games.