I've replayed both Zero Mission and Super Metroid (twice each) recently, and can confirm that Super is better. By a lot. It's got better atmosphere, better story, better music, better physics, and doesn't have a Zero Suit section. I'm puzzled by people who prefer the jumping in Zero Mission. When you jump from a run in Zero Mission it slows Samus down for some reason and it feels rubbish. She keeps her momentum in Super a lot better and when you work out her controls it feels much more organic. Also as a bunch of jumps in Zero Mission are designed for the ledge hang you seem to constantly be slowing down. Little things like the second you let go of the jump button in Super Samus starts dropping gives you Mega Man level control of her vertical height. All of these complaints about Super's physics are workmen refusing to learn their tools.
Also, the sequence breaking in Zero Mission is all preordained by the devs, it's (again) not as organic as Super.
This isn't to belittle Zero Mission, it's an incredible reworking of Metroid. It's just not the king.