I disagree with Super Metroid though because the controls were very intentionally designed by the developers to be the way they are. If you look at top level players of the game the skill ceiling is so much higher than a lot of other games because of the way the controls work. Even just seeing the improvements in the way players play the game now compared to how they played it back when I first ever saw a speed run of the game, back when the record was like 55 minutes or something is pretty wild.
I'd prefer some awkwardness knowing with enough mastery, you could play the game like that over something that feels better or easier.
My biggest issue with Zero Mission was the weightiness of it. In Fusion it made sense because it was an artificial environment in a space station but Zebes already had two games establishing gravity was lighter there and things were floatier so it always bothered me it was like that in Zero Mission. I agree though, Metroid's controls were never great and Zero Mission itself is so different from the original anyway the improved controls aren't really even the biggest reason why it's easier. It's more the lack of janky nes bullshit.
Metroid 2's controls really weren't that awful for a gameboy game and honestly improved the nes ones a lot. The biggest problem with Metroid 2's controls was the spider ball. I remember it being annoying as hell to control.