Kaijima said:
You are a woman in a super suit.
You enter a space station.
People should not shoot up space stations.
That makes holes. It breaks things. Air goes out. Systems fail. Everyone dies.
The *dude officially in charge* tells you to stow yer dangerous shit until he gives the word.
You are a professional, and not a gamer who just wants to shoot everything to see what happens. So you follow that order.
How does this not make sense?
Yeah. The power-up that does literally nothing but protect Samus from burning to death is a serious danger to other people on the ship. So is the one that does nothing but negate effects on gravity. Oh, and the grapple beam, Samus is just gonna accidentally kill everyone around her with that thing.
Even ignoring that, it still doesn't make sense. If her weapons really are so dangerous, why would Adam let her continue using them after it was necessary? If they were so horribly dangerous, wouldn't it make more sense for him to authorize the weapon use on a situational basis? "Oh, you need to shoot that switch through the wall? Okay, use your wave beam for this. But then turn it off afterwards."
But instead, it's, "Alright, whatever, I have arbitrarily decided that this weapon that was horribly dangerous to everyone around you is no longer horribly dangerous to everyone around you just because you encountered one obstacle that requires it to pass. Go ahead and use it with reckless abandon."
Not only is it an irritating mechanic, it doesn't even make sense within the context of the game.