It all sounds to me like bad writing, the plot had never been that important up until other m, so Sakamoto was having no problems. Then he decided he should make a game where he actually fleshes out Samus' personality, then fell flat on his face having to do real writing. I'm not a big fan of the series myself, so maybe he was great at writing until other m.
Previous Metroid games were more about the gameplay. You didn't really have characters sitting around, discussing their childhood or reminiscing about past relationships. You basically spent the game running around, solving puzzles, and blasting badguys.
But this, in itself, crafts a personality of sorts. You get the idea that Samus is on her own out there. That she's got nobody to call in for backup. That she dove right into the lion's den without a second thought. And that she's too busy kicking ass to spend time on flashbacks.
Other Metroid games did have some plot to them... There was some backstory about who Mother Brain was, and what a metroid was. And you had the whole thing with the baby metroid... And the stuff with the phazon and the shadow Samus and stuff like that... But you never really had Samus doing a whole lot of chatting or introspection or anything.
And that, in itself, creates a character.
Look at someone like Gordon Freeman, in the Half-Life games. I don't think he's ever said a single word. You know stuff about him... People talk to him... He does lots of stuff... Saves the world a couple times... But he doesn't say a single word. So you get the impression that he's a quiet guy. Maybe he's socially awkward, maybe he stutters, maybe he's just too busy kicking ass... Whatever. But he doesn't talk much.
It allows you to fill out the character with some of your own personality. You can fill in your own comments and remarks, instead of listening to the game supply them. You can decide, to a large degree, what's going on in the character's head. In some respects Gordon Freeman isn't a separate character with his own personality - he becomes a suit for the player to wear.
And then the developers suddenly decide that they need to flesh out the character.
And this silent protagonist suddenly starts talking. And starts having flashbacks. And starts reminiscing about that time in band camp.
And not only is that character suddenly chatty... But they're suddenly behaving wrong.
Samus has killed Ridley in pretty much every Metroid game there is. By the time Other M rolls around, she's killed him off something like 4 times. And suddenly she breaks down and regresses into a child. Why?
That'd be like Gordon Freeman suddenly breaking down and regressing into a child when he sees a headcrab.
Fine... Attribute it to bad writing if you like. Maybe it makes more sense to attribute it to incompetence than to malice. And no, it doesn't have to be canon. But it still makes for a lousy storyline and some horrific characterization.