It's a compelling argument, and I definitely agree that the Metroid Prime only sees Samus as a violent entity. At the end of 'Metroid Prime' it only takes the Phazon suit: the armour and the weapon system, nothing that would allow it to learn her mentality or even her biological structure (its appearance in the final battle of 'Echoes' goes on to show that its understanding of human biology may be sketchy at best).
Concerning the issue about whether or not the warning to expel Phazon comes from the game or the power suit, I'm going to have to replay the game and find out exactly what font it pops up in; I know the game's tutorial prompts appear in a different font to the one used for the messages that appear to give the player directions on where to go next, and this is used to differentiate between the two 'vocies.' I'll let you know what result I reach. Either way though, if not specifically the visor, the power suit still gives Samus a unique advantage over the other hunters in controlling her Phazon corruption: it links the PED directly to her cannon. We never get any specific information on how the other hunters' abilities work, but they lack any overt means of getting excess Phazon out of their bodies.
Moving on to Ghor's highly mechanical composition giving him an edge, I'm going to make a bit of a deductive leap here by making the following statement: Ing possession in 'Echoes' was the prototype for what happens to the hunters in 'Corruption.' This is supported by how the particle effects for Dark Samus absorbing each of the dead hunters is almost identical to those seen in 'Echoes,' when an Ing parasite attempts possession of a host and also by how the nature of Phazon has changed between the original 'Metroid Prime' and 'Corruption' (in 'Prime' it causes mutations and psychosis but not direct control. In 'Corruption' Ghor assists Dark Samus' agenda by sabotaging Samus' efforts to repair the Skytown Aurora unit, and Gandrayda appears to actively work with the pirates - Dark Samus' other pawns - to set a trap for Samus). The Ing had no trouble controlling machines whatsoever, consider Quadraxis for example.
As for Samus' resistance to loss of free will resulting from Phazon possession, again my knowledge is a little lacking in this but I'd refer back to 'Echoes,' and inquire whether Samus' resistance to Ing possession was attributed to the Chozo power suit or to the Luminoth energy transfer module; if it's the former then that would suggest her resistance to Phazon is due far more to the technology she has at her disposal than to her willpower. Either way though her resistance to a different form of possession is definitely linked to a piece of equipment, not strength of mind.
I'm not contesting that Samus is a grade above the other hunters, the Federation acknowledges this, the other hunters acknowledge it in their own way, the Metroid Prime acknowledges it by taking her form without any changes even after having access to all the other hunters. Your point about her staying conscious long enough to use the planetary guns to shoot down the first leviathan seed stands. That said, there is a lot in the series to support that her power suit is a tremendous contribution to her efficacy, both in lore and in game-play. In terms of lore, the pirates spend most of the first game in the series trying to reverse engineer the technology of Samus' suit (this becomes less relevant by 'Corruption' because they're all working with Phazon instead), they manage to crack some of the weapon systems towards the end of the game. In terms of game mechanics, the games center around acquiring new utilities and new weapons for the power suit, not the character. This is the metric by which the player charts their progress, not the development of Samus as a person.
The last thing that makes me sceptical with regards to Samus' victory over Dark Samus being allegorical to her conquering her violent nature is that the character herself seems largely oblivious to the whole message that you suggest the game carries. She shows remorse for the other hunters she had to kill in the closing cinematic, and you aptly pointed out the frustration Samus displays at Ghor's death, but she never seems to question the nature of war as an institution at all. The whole Prime trilogy started when she was, without contract, hunting down Ridley on the frigate Orpheon. Samus is a bounty hunter. I admit that in the universe created for the Metroid franchise this isn't quite as morally grey as it might be in other universes - the space pirates have never been exactly what you'd consider sympathetic - but this is someone whose livelihood stems from violence. There is perhaps some credence to an alternative viewpoint if you apply the theory of a 'just war,' Samus fights to protect the Federation from pirates, to protect U-Mos from the Ing, tries and fails to protect the other Hunters from Phazon. Ridley is the exception, but since we're rejecting 'Other M' as canon there's not really much to expand on that.
I agree that dumb luck doesn't exist in fiction, but on the flip side fiction is full of characters who are made special more by the items they've come into contact with than any virtue of the characters themselves. As examples I would put forward the Prince of Persia and the Dagger of Time, Zael (from 'The Last Story') and the power of The Outsider, the Nanosuits in Crysis. List is not exhaustive. Don't get me wrong, these characters weren't average to begin with, but they weren't remarkable either. Furthermore the illusion of dumb luck does exist; since you stated fiction in general as part of the premise I'll accept the invitation to deviate slightly and reference 'Half-Life 2: Episode 2.' Consider for example the two encounters Gordon Freeman has with the Advisors: in both cases his survival can be attributed to dumb luck. He was never actually going to die; protagonists don't die in such pointless, underwhelming circumstances (unless you're in a novel written by George R. R. Martin but that's beside the point) but from a purely plot-armour disregarding viewpoint, it certainly doesn't come down to anything other than luck. Frequently the storylines contain elements of the character developing beyond being dependent on these things and becoming remarkable in their own right, but the Metroid Prime trilogy never seems to do that, unless you count how Samus loses most of her suit's capabilities in the opening sequences of 'Prime' and 'Echoes.'
I think to some degree though the very nature of the media form kind of impedes this kind of message getting across. Players know they can't die in cinematic sequences that couldn't be avoided. A player doesn't look at the explosion that damages the power suit on the Orpheon in 'Prime' and think 'I got lucky there, that could've killed me,' they just accept that it happened the only way it ever would have done and move on. It's the same story concerning surviving the crash on Ether's surface in 'Echoes,' not being stranded on Elysia after Ghor smashes up the gunship in 'Corruption.' The format of the medium eliminates any real sense of peril. The exception to this is Phazon corruption, because it appears in the game's mechanics as a non-standard game over, and because it progresses along with the narrative at an appropriate pace for Samus to succumb to corruption as she completes her mission. (I'm aware I'm trespassing a bit on credibility here, we know Nintendo's not going to kill off all chances of a sequel to one of its longest running franchises) In terms of what is strictly within the narrative these were all lucky breaks for the character; none of them really had anything to do with Samus' skill or resilience.
On the topic of your Youtube series: Are you planning to do any third party titles or are you sticking to IP that Nintendo owns? I ask because I'd really like to see what you make of Xenoblade Chronicles; there's a lot of material there looking at themes of self-identity and prejudice, as well as the ideas of the destructive nature of power without direction and a sword being an extension of the soul that you summarised in your analysis of 'Ocarina of Time.'
Excuse a few spelling or grammar errors please, anything not attributed to the differences in spelling between English (UK) and English (US) should be explained by the 2:30 am time of this posting.
I'm actually very familiar with Joseph Campbell, and he certainly is a good pretentious thing to reference. 
