It's the best one. The story is pretty much left to your imagination, unlike in Fusion, but I think it's all the better for it. Fusion has the advantage in controls but Super has the better gameworld and exploration. They're both excellent but Super has the purity as the current king of the franchise. You should definitely pick it up on VC. It's only a fiver, anyway.
It's nothing like the original metroid. I too played that on GC and found it unpleasant to play. Anything beyond Snes is like that for me though.