Hmm.... I will say it's definitely a different take on the plot, and makes a far more cohesive case for sexism, but rather i agreed with the whole "frayed writing" rationalization rather than any sort of mysoginist conspiracy. We have to recollect that the relation between storytelling and gameplay has always been ... loose even in the best Metroid games. Samus has always lost her powers in very peculiar ways, but the best times always ignored it (Metroid II, Super Metroid, Metroid Prime 3) rather than coming up with plot devices that should naturally have led to her getting killed, as in Metroid Prime and Metroid Prime 2. Metroid Fusion actually deserves credit here, because the infection of her and her suit led to a very plausible reason for her to go back to square one.
In Other M they tried something different, and i imagine part of the utility of this was to minimize front-end exploration, though they could have conceived of other plot devices for this (for instance, Samus could have had to download her old powers at the save stations, a device introduced in Metroid Fusion as well), and they could have added in the idea that her use of the Hyper Beam at the end of Super drained her suit of all capability (though that would throw the escape run of Super into canonical hell)
As for the Hell Run, the author here gets it right the first time before attempting to piece it into his/her conspiracy: it's a gameplay challenge at its core, one that could have been better explained, as many things could have been better explained, but at its heart is no more incredulous than "The Ing assaulted me, stripped my suit powers, but for some reason left me alive"
As for the shot-in-the-back scene, i too was baffled at that entire turn of events initially, until i came to the understanding that he "had" to shoot her, knowing that she would try to stop him and was more than capable of stopping him. Adam correctly assessed Samus' cowboy tendencies, but knew this was one mission no-one could come back from alive. Again here's another scene which could have been done another, better way, but is understandable in context
Samus showed even in this game that she had an independent streak when authority crossed with morality, mostly near the end of the game in this case, and near the end of Fusion, but Adam was an authority figure she respected, and she wanted to show that she had grown out of her pointless-rebellion phase. Simple, but poorly portrayed to create something that looks kinda like a mysoginist conspiracy if you squint at it right