I haven't played the game, and don't really plan to, but from what I've heard Other M was just badly written and did not characterize Samus as a character properly. I'm sure they could have done much better with it. It's really just Team Ninja not handling the source material properly.
The thing about "projection" is that sometimes it helps the character develop more. Not everything absolutely has to be explained via text in a game, you can make characterization from the gameplay itself. AKA: subtlety
Lets look at Shadow of the Collosus. Wander brings a dead girl to a forbidden valley to bring her to life, this indicates that he holds deep feelings for her. In gameplay, he can barely hold the sword or swing it properly, yet he can aim a bow and arrow very well on horseback, indicating he's possibly a horse archer. When he falls down and experiences extreme pain, he doesn't get up immediately, showing that he's not a superhuman yet he's willing to slay these huge collossi just to bring a girl to life, showing he's stubborn, never letting go. None of this is "explained", but you can easily deduce this from the gameplay itslef.
If, in a sequel, Wander was portrayed as a spoiled brat who's heir to the throne and he hates his father, that would be a pretty jarring change in character (not saying Other M does a change as significant as that, just an example). While we may know nothing of of Wander's character, nothing in the previous game indicated a past like this, so unless they play with it really really well, it's not going to slide.
Now with Other M, think of the other Metroid games (I've played a few of them, but I'm gathering this from other impressions). The games are all about exploration, isolation, and lonliness. You explore vast environments in foreign planets, not a single human soul in sight, your only companion is your arm canon. Because of this, you can assume that Samus has rarely had human contact, more or less a loner. Samus is revered as a fearless bounty hunter (apparently), so you can assume that she's independent and "plays by her own rules", and in fact in Metroid: Fusion (so I'm told) Samus is given orders by a computer, but she even states that she dislikes taking orders, again a sign of independence.
With Other M, apparantly none of that get into play here. She's portrayed as weak amongst superior males (apparently, again, I haven't played it, just trying to see it from their perspective) and she deliberately takes orders. She's a fearless bounty hunter who plays by her own rules (we can assume that through gameplay) yet she is shown as being subservient to another's orders. While, as you said, we know next to nothing of Samus as a character through general story, you can deduce and inference her character through her actions. Her actions build her character, not her gender.
I don't know if any of that is true, as I said I'm going from what other people have played of the game (I've played some Metroids myself), but overall I can see where people got the idea that Samus was an isolated, lonely character and an independant woman considering that women in video games at the time was unheard of. Just because we "projected" our own ideas to the character does not mean that they're wrong to assume that. You don't need extensive text boxes of backstory to define a character, you tell who somebody is through their actions.
I've never heard of the argument that "because it's made in Japan, it's sexist!" or whatever you said, or that Samus must be stoic/emotionless terminator. Just that Team Ninja didn't do what it could to developer her properly. Samus may very well have had daddy issues or have strong maternal feelings out of something she willingly gave up to lab experiments (from what I've been told), but from what I can tell, Team Ninja didn't really do a good job at presenting it.
r (though I hope you do), just because we were never explicitly told about Samus as a character, there's still a lot you can inference from the Metroid games. And you could go all meta with it saying "Samus is obedient because she's following our orders on her!", though that really doesn't hold up since, well, how else are you going to play the game?
