Well, Samus is fully powered up at the beginning most Metroid games but loses her powers in an explosion. I really don't see how "she decided not to use them out of respect for a commanding officer" is that much worse than "because she exploded again."
It's much worse. Does it really need to be explained why having something taken away by force is vastly different than not using it by choice? They could have easily worked something into the story about how her powers got disabled somehow, and then throughout the game you pick up repair kits or something like that which could reenable them one by one. That would have been far better than Adam saying you "now have permission to use this which you had all along, but I prevented you from using just because I'm an asshole." When I first played the game I genuinely believed Adam was the bad guy and he was doing this just to sabotage the mission deliberately. Later cut scenes revealed he actually was a good guy, but there is never any good justification given for why he forbid Samus to use her powers.
The Super Missile I can sorta understand because it has the potential to damage the station, but give me one good reason why the Varia suit was forbidden.
Edit: also she doesn't die and fail the mission because of this if you, you know, beat the game.
I beat the game, but I died a number of times before that happened. The funny thing is when Samus dies Adam's voice comes on the intercom thing and seems distressed over her death, even though he could have prevented it in many of those cases by letting her use her powers. Again, give me a good reason why the Varia suit should be disabled. Adam doesn't authorize it until AFTER you have to go through some fire level where you take damage the whole way through. Why the hell wasn't it authorized BEFORE that?
I understand the point is to add a challenge to the game because having all powers from the beginning would make it too easy, but they needed to have some sort of plot device that logically explains why the powers are gone. Just having them disabled "because I say so" is a lame cheap shortcut way of doing it, and it genuinely does effect my enjoyment because I can't get past how stupid it is. Adam was an asshole for not letting Samus use even the defensive things like the Varia suit, and Samus was an idiot for going along with his orders.
Later in the game there is a point where she loses contact with Adam and enables one of her powers without his permission, but this was too little too late. She should have used her own discretion from the beginning. How the hell can she be a Bounty Hunter and yet need someone like Adam to hold her hand and order her around and tell her what to do? This ties in with the part where she breaks down and cries. If you take those two things together it makes you wonder what business does she have being a bounty hunter at all. This is nothing like how she is in all the other Metroid games... Sakamoto took the once mighty Samus character and twisted it into some feeble helpless baby who cries and needs a man like Adam to give her orders. This was incredibly offensive and sexist, imho.