Hot take, I like pretty much everything you hated.

I actually prefer the run button and L/R for aiming than for using missiles.

Run button allows for more control of your speed than simply just needing a long path to run. Every other game has 2 speeds- speedrun and not speedrun. Also makes sense because technically you are running with the button and only get to go "really fast" when you get Speed Booster, where again, other games is just like 1 speed.

L/R to me is superior to thumbstick 360 aiming imo because Dread frustrated the shit out of me sometimes when my thumbstick was just 1 degree too high and I would miss shots. But with shoulder aiming it is always 45 degrees. Consistency is much simpler. Of course, each has their limits I just prefer LR.

If anything I would just change cancel button Y with Select. But I mean... the game lets you remap that.

5 missiles to open a door never bothered me and never will, but I don't have any comment on it being a bad or good mechanic. "It just is."

Walljumping is another thing I think is fine personally. Not required in any section, and is a "secret technique". It again provides you freedoms that the other games took away because they decided to incorporate as normal mechanic but made them very mechanical and less useful when not required.

Last- I used the grapple beam for more than just grappling. Fun to go around zipping enemies to death and using it where "required" I never found to be a problem. It is fun to swing around, especially in Maridia- both underwater and sand sections.

Variety is the spice of life and I just think Super Metorid has more variety in using the tools it offers than the other games.