Oh not this bullsh!t again. The whole reason Samus listened to what Adam had to say is because he and his troops were on a search and rescue mission to find any survivors as well as gathering evidence on what really happend and he didn't want Samus using anything that might destroy evidence or accidently kill survivors. Since Samus has respect for Adam she agreed to only use her weapons when he feels it's right since she trust his judgment. Yeah, there were some parts that make no since like why it took to get the varia suit, but the whole reason behind this part of the storyline anyway is Sakamoto wanted to find a more logical reason for Samus to not have all her weapons from the start and this is what he thought was the most logical way. People have to stop getting so hung up over this part of the game since the entire reason is just to give Samus a new way of getting powerups as she progresses.
Personally, my whole problem with the "Permission" system is that it's incredibly contrived and stupid, and it doesn't even make sense within the confines the story gives it. OK, Adam telling her to deactivate Power Bombs and maybe the more powerful beams makes sense. That's powerful stuff that could blow up the station if not used carefully. But forcing Samus to deactivate her armor, Grapple Beam, etc.? It makes absolutely no sense why these lesser tools were forced off as well, within the logic of the story. Frankly, I don't understand why Sakamoto felt the need to justify why Samus has to be powered-down at the beginning of the game. We all understand that that's just a gameplay contrivance of the Metroid series, and while it can be neat to see an explanation (the best being Metroid Prime's) I don't really give a damn if it's not. It's like throwing a fit over why the Mario games never explain why Mario doesn't just start the game with a full inventory of past Power-ups, which then have to be stolen from him by a Lakito in the first 5 minutes of the game (or like complaining why Link isn't uber-powered up at the beginning of the Zelda games featuring the same link). I'm willing to give the gameplay contrivance some lenience, because if I don't the game falls apart.
Throw in the seemingly random times that Adam unlocks your equipment, and the system just doesn't make any sense. Sure, it's somewhat sexist as well, but that aspect of the system is incredibly minor (and can be explained more or less decently by the story) and far outweighed by it just not being a good gameplay system in general.
Now the Ridley was just bad writing on Sakamoto's part since she's dealt with Ridley two times before in his canon
Actually, at that point in the Metroid canon, she's killed Ridley 4 times in various incarnations.
1. Metroid/Metroid Zero Mission.
2. Metroid Prime.
3. Metroid Prime 3: Corruption.
4. Super Metroid.
I know that Sakamoto doesn't like to acknowledge the existence of Metroid games that are better than the ones he's made himself, but there's no reason we shouldn't.

But yeah, the Ridley scene was the one that destroyed the game for me, because it is the one aspect of the game that is blatantly, overtly sexist. Maybe it's just a Japanese societal thing, but I don't think we'd ever see (in that same situation, with that same history) the main character crying in terror and curling into a metaphorical fetal position if they were male.
Maybe if this was Samus' first run-in (rather than her 5th) with Ridley, I could buy it. But it's not, and it's terrible writing.
I really wish we could put Metroid Other M's incredibly poor writing and design behind us and chalk it up to an insane (and, IMO, incompetent) director being given free reign to do whatever he wanted. Hopefully, Nintendo will soon announce a Sakamoto-less Metroid title so we can look to the future instead.