Firstly, haven't played the game, but even so there's a few things that stand out from that video commentary as being a bit off. To begin with, the arguments that contradict the speaker's viewpoint are largely oversimplified. From what I can tell, it's not that Samus is taking orders from a man that the average player is irritated by, it's that she does so to the detriment of her own common sense and at a great personal risk for no better reason than semantics.
The other thing is that grabbed my attention was the assertion that the gamers' perception of Samus' character prior to its definition in Other M was based purely on projection. Rather than blatant selective use of facts I'll put this down to the speaker's ignorance of the Prime games. Repeatedly Samus is introduces as a bounty hunter. We know therefore what line of work the character pursues and this in turn says something about the character. Whether or not it is true that a bounty hunter is someone who prefers to work alone and, most pointedly, eschews a regular chain of command, that is the perception that the average gamer has of the profession. (probably due to the most famous sci-fi bounty hunter, Boba Fett, more or less being the archetypal illustration of the description) Doubtless being aware of this stigma, the developers of the Prime series' decision to mark Samus as a bounty hunter deliberately cultivated these perceptions of the character. Unless I missed something, there was never a formal declaration of the Prime trilogy being non-canon, therefore that characterisation stands.
Now, as any player of the later Legend of Zelda games will tell you, a silent character doesn't have to be two dimensional. I would argue that the same is true of Samus in Metroid Prime 2 Echoes and more noticeably in Prime 3 Corruption. Consider Samus' reaction to finding the dead troopers in Echoes. We know what her visor is capable of, I consider it unlikely she was checking that the commander was dead. Consider also the hidden ending cinematic of Corruption in which Samus is seen on Elysia thinking of the other hunters, now dead. This shows a sensitive side to her character that couldn't even by the most harsh of observers be seen as weakness; unlike her portrayal in Other M, or so I've heard.
Which brings us to the infamous Ridley scene. The main defense by the developers (and the speaker in the video review) is that her reaction is a realistic portrayal of PTSD. The gamer's argument is that realistic or not it's inconsistent with the character. I'm sort've on the fence here as while Samus has never frozen up when confronted with Ridley before she hasn't always acted rationally. The first sighting of Ridley on both Prime games in which he appears prompts a scene in which Samus makes a stupid decision. Firstly, when found on the space pirate frigate, Ridley's appearance causes Samus to momentarily forget that the ship is exploding around her as she instead stops to watch her nemesis make his escape. (I don't recall whether she actually shoots at him as well) Similarly in Corruption at the second power generator Samus, caught off guard and at a disadvantage, attempts to stand her ground against Ridley and consequently is hurled into a pit leading to the planet's molten core which would almost certainly have resulted in her death were it not for Rundas. (odd that there were no cries of 'ruined forever!' on this instance of Samus being saved by a male character despite Rundas' 'now you owe me one' comment practically lampshading it.) Now why the script writers didn't do something similar in Other M I can't say. I agree that the way they chose to handle it had some unfortunate implications, but I don't believe it was as out of character for Samus as some people are suggesting.
The largest problem as I've heard it told is gameplay and story segregation. As far as the character is portrayed in Other M the player is hard pressed to believe that the same character who is showing such emotional insecurity in the cut scenes would be capable of facing down the terrors that stalk the derelict ship, much less have the motivation to be there in the first place. Referring once more to the Prime trilogy, I would question whether the same character portrayed in Other M would be capable of soldiering on after finding herself trapped on a hostile planet with the people she was sent to save lying dead on the ground (Echoes prior to meeting the Luminoth) or after just puking phazon onto the ground (Corruption).
Now it's possible that we're not giving the developers enough credit. Perhaps they were indeed taking a great risk and angling for the line that someone who does not know fear cannot be courageous. If courage is the act of conquering fear then those without fear are incapable of it, or so the theory goes. If the developers were aiming for this though they made a mistake. Such an angle is ambiguous unless clearly stated, and here it's only implied if you're aware of the philosophy and looking for it.
EDIT: 'scuse the wall of text there.
EDIT2: Ah crap, just noticed the comment above about Team Ninja not being responsible for the script writing, gimmie a moment to change where the accusatory finger is pointing. XD
Should all be good now.