SPOILERS ahead (can't change this topic's title and it's already spoilerific):
I've got some things to say here. Speaking of that last post, corneliab: "She Got Over It"--people can regress given the right scenario. Just like PTSD.
Let's look at the context: Samus went from a lone bounty hunter to a compassionate/vengeful mother-figure in Metroid II's ending and Super Metroid. (She was never as hard-nosed/earthy as Alien's Ripley, or she wouldn't have sympathy for baby Metroids...or for that matter the trapped Dachora and Etecoons). In the end, she lost the baby, despite her best efforts; it had to save her. Following this lost feeling of connection with the baby, she's thrown into a situation where she is united with the only other people she's had significant connections to in her life: Adam and Anthony (and to some extent by proxy, Adam's little bro, Ian). This awakens the other, younger side of herself that struggled so hard to fit in after being an orphan--the only other time she really dealt personally with major social situations. As the mission goes along, she is surprised to run into Ridley--who is connected with not only stealing her parent's lives, but also indirectly responsible for the baby Metroid's demise, as well. She offers to face Ridley without Anthony, wanting to protect him like she wanted to protect the baby. But as she sees Ridley amidst the flames, it triggers the wealth of emotions she has built up from revisiting her past already during this unsettling Other M mission. She was sure she'd never have to face Ridley again after Super Metroid (which was after Primes and featuring a real Ridley, not Meta Ridley, etc). Is it carried off perfectly? No. Does it destroy the game and Samus? No. (It's interesting that no one complained when Samus teamed up with bounty hunters and GF marines in Prime 3--and needed their help to advance/survive--and then was sad/wistful about it in the best ending).
Speaking of which--You bring up the Prime games, which is understandable, but those don't register with Sakamoto (who mostly worked on Metroids 1, 3, and 4). Those are secondary canon to him, and thus didn't play into his main timeline story whether they should have or not. Even so, the scenario I laid out would be the perfect opportunity for a PTSD moment more so than in the Prime games. Especially so, again, when you consider that the Prime games occurred BEFORE the loss of the baby in Super Metroid and the facing of a second non-Meta Ridley.
As for the manga--It's information has been incorporated into the games for a while. Metroid Fusion's Japanese endings feature young Samus training with the Chozo and also (if you get < 4 hours) show her parents' last stand against Ridley with her as a child cowering. Further, Metroid Zero Mission features more childhood teases with the Chozo linked to the manga. The manga speaks of how the Power Suit is linked to the mind, explaining why the suit failed on Samus during the fight with Ridley in Other M. The Prime games only further link her history, past and present with the Chozo. Her power-ups are linked to Chozo tech, as is her Power Suit. And you see how obsessed she is with the thought of Ridley when she basically is tracking a version of Ridley for the whole of Prime 1.
In Fusion, it was clear that Samus was an introspective woman, and it makes sense that she'd be thinking/pondering with all the puzzles, Chozo ruins, and battles she's been engaged in over the series. Her mind can't be a complete blank when she's doing the amount of exploring she has. I'm in the last quarter of Other M, and while the story could have been handled better, it doesn't ruin the character or world of Metroid. I haven't beaten it yet, but I'm more confused about how Other M's treatment of GF experiments affects the novelty of Fusion's big reveals with Samus herself. But I'm not going to hold that against the whole package. This game is really opening up now, and I'm losing myself in it.