I've read that article, and I think the author misses some rather obvious counterpoints to his conclusions.
1) Adam disables Samus so that she can't stop him from sacrificing himself. It's a common enough trope -- more frequently seen in shounen series, it does feel out of place in a Metroid game.
2) Adam does answer Samus as to why he shot her. He just did it in a typically indirect Japanese way, by starting his explanation with background details ("Those metroids can't be frozen, therefore you can't stop them, therefore I ..." etc) rather than starting with the main thrust and reasoning backwards from it, which is what English-speakers are more used to.
3) Many instances the author points out of Adam being verbally "abusive" or dismissive of Samus are clearly just him being all, for the lack of a better word, tsundere. Adam's personality is a fairly common archetype: a man who expresses his guarded emotions indirectly by kind of picking on the ones he cares for but in an endearing way. (Like the main character from Kanon.)
But other than that, the author makes a convincing case -- entertainingly so, because it shows just how bad the writing is. I don't believe for an instant that Adam and Samus had an abusive relationship, but the fact that someone could so convincingly interpret it that way was worth a good laugh or two, much like a Cracked article.
But what is up with this quote?: "If the game?s creators think that there is more to the experience of being a woman than being an emotionally-driven womb with legs, the game doesn?t really seem to acknowledge it." Are you kidding me? All of the women in the story are successful career women who outshine all their male counterparts, in fields typically dominated by men, and are the main drivers and foci of the story to boot, while the men are basically expendable. As soon as I see the author write a rant about how sexist One Piece is for portraying all men as over-emotional sentimental idiots who fight each other at the drop of a hat, then we'll talk.
I mean, just look at how men are portrayed in Other M. They get picked off like flies and we're not supposed to shed a tear for them -- the women at least get to be the objects of sympathy and tragedy. They get the sympathetic spotlight, while the men as a class seem outright sinister: that evil doctor in the beginning... the evil colonel at the end... heck, all the men Samus is with except Anthony seem shady enough to credibly be the assassin. And if the women have "catastrophic failures of judgment", what about the overarching massive failure of judgment by the GF male hierarchy that is the decision to replicate metroids and space pirates in the first place?!
I just ... don't think there's a case here. Samus's portrayal may be disappointing relative to what she seemed to be built up as by previous games, but can't we just leave the sexism card at home?