So, do you use Select for Dash for something?
Like I said, if you played Super first and built up that muscle memory with a more cumbersome system, I can understand preferring it, but no matter how you slice it you're pressing more buttons for the same functionality in Super Metroid. One button to switch to missiles, another button to shoot them and a third button to cancel them is just a clumsy and inefficient use of the controller, and the GBA games solved that problem perfectly.
Admittedly you still have to use Select to switch between supers and regulars in the GBA games, but you don't really need to rapidly switch back and forth with missile types like you do with your beam and missiles. I pretty much only use super missiles for green doors and bossfights, and when I'm fighting a boss I generally just want to use supers until I run out. Meanwhile I'm pretty much constantly switching between the beam for charge shots or shooting down projectiles or weaker enemies and missiles for stronger enemies or boss weakpoints.
I guess I just don't really have a problem with diagonal shooting not having two dedicated buttons. You can shoot diagonally up or down with the D-pad alone; I honestly can't think of many other sidescrollers that devote even one extra button to diagonal shots, let alone two.
Also, yeah, what button do you use for Dashing if you have both weapon switch and weapon cancel mapped to the face buttons?
Run is set to L
Aim up is ZR
Aim down is R
Missile select is A
Cancel is X
Shoot is Y
Jump is B
Nothing cumbersome about that setup at all (though the default controls do suck pretty badly). I like having speed control, since there are times when I don't necessarily want to speed boost, and I like being able to freely blast missiles without having to hold a trigger to do it. For something like a Ridley fight, where you're going to be emptying your entire missile supply, I think Super's system is better. Not having to hold that extra trigger to shoot does make it easier to aggressively wall jump and aim up and down simultaneously. If you're just quickly blasting a door open, the GBA system is better, but in those casual situations it doesn't really matter. I'm fine with tapping a button, and like I mentioned, if you tap while holding X it cancels itself after firing.
There are other things I prefer about Super, like the jump physics. I like the potential for adjustment and building momentum Super had; the GBA games made Samus feel very heavy and every jump feels pretty much the same. The wall jumping is also a lot stiffer in those games, especially Fusion. I do like the corner grip and shinesparking expansion those games added, though.
I guess what I'm trying to say is that I've never been bothered by Super's system, but the GBA games regularly get on my nerves. And I've put enough time in them that it's not an issue of bias. I'm not saying they didn't make improvements, just that I still prefer Super overall. Hopefully Samus Returns will have good enough controls that it surpasses both styles.
Some of you are really throwing shit at the wall to make it look like Other M is anything but unadultered crap.
Say what you want about Other M, but it at least had the basic principles of exploration, powerup collecting, and atmosphere that the series is based on. It didn't execute any of them well and subjugated them in favor of storytelling, but it had them. Federation Force didn't even attempt to base itself off any of those things.