I'm not going to argue with you about the psychological aspects of Other M's story. What I am going to say is this: It's terrible writing and the series was better off not touching it.

Part of the problem is where the events of the story fit into series canon. It's after Super and before Fusion, both of which are games where Samus takes Ridley on in single combat and wins. In neither game (Or, indeed, any other title released before Other M that features Ridley.) does she display any visible trauma or fear at the sight of him. So if her freak-out in Other M really is PTSD and not just Sakomoto's failed attempt at melodrama, then how do you explain her calm composure in all their other encounters? Does her suit keep her on a drip of some kind of future-space medication that prevents traumatic episodes that was malfunctioning at the time? If that were the case, some indication would have been nice.

And then there's the game's central theme of motherhood (We don't need to go over that, do we? The acronym, the subtitle's anagram, the clumsily handled fictional class of distress signal and bottle-ship shaped like a baby's bottle...). I don't have a problem with that in and of itself, but like so many other parts of the story, the ball was dropped so hard it bounced up to the moon. Samus' sudden attachment to the metroid hatchling to the point of referring to it frequently and exclusively as "The baby" comes right out of left field. Did Sakomoto just forget that, in Super Metroid, her first instinct upon "the baby" imprinting on her was to hand it over to scientists? If she had felt maternal towards it all along, then she has some fucked up ideas about parenting.

I'm all for the psychological exploration of video game characters (I wasn't upset when Tetra from Wind Waker ended up getting kidnapped after finding out about her heritage so much as I was at the fact that her existential crisis was worked through entirely off-screen. ), but it's important for such development to fit within the context of the overarching story and also not actively contradict prior (And chronologically, future) events.

Also, just because the author of a work doesn't intend for a message to be present, doesn't mean it doesn't show up. I highly doubt Stephenie Meyer, when she sat down to write Twilight, said to herself "I'm going to write a story romanticizing obsessive, abusive relationships!" but anyone who can look me in the face and tell me that that's not pretty much exactly what the series does is either lying to themselves or only knows it from what fans have said while gushing about it.