For your theory to work though, that would imply that the fanbase was in disagreement over who Samus was, which is not the case.
Not at all. I'll call it the Bobba Fett syndrome. A character that literally had no characterization outside Vader going 'Yo, this dude bad', but people latched on to him as this badass bounty hunter. There is literally nothing in the original movies that implies that, and in fact, his original death seems to imply he was far from badass, and probably meant as a bounty hunter who happened to get lucky and have the right friends (of course Lucas tried to recton all this when he realized how marketable the character was, but looking at the original films, it's an unavoidable conclusion).
If you want an example closer to home, let's look at Zelda. Almost everyone hated the characterization of Link in that old 'toon from the 80s. And why? It didn't match what people thought. They thought he was some kind of warrior in the vain of, I don't know, Aragon or something. Not some perverted kid who happened to be good with a sword. And there's nothing,
nothing in the Zelda titles to make anyone think he would be either. He's a nothing character, pretty much like Samus, but over time people have slapped certain stereotypes to them that there becomes this psuedo-characterization that a lot of people adhere to, but there's nothing within the actual games to support that outside 'a silent loner', which people often misunderstand, anyway.
In short, a lot of people saw a Han Solo sewed upon a featureless doll, and got mad when that was peeled away to be a Luke Skywalker.
In general people agreed that she was the strong silent type who enjoys solitude and the independence of being a freelancer. Hardly anyone in the fanbase would have contested this, and yet when Other M came out, the version of Samus we saw was not compatible with the previous assumptions about Samus. Other M's Samus is much more timid, has serious detachment issues regarding Adam, and is shown to have been excluded socially rather than being someone who chooses to be alone. Forgive me if I find it a bit hard to believe that Metroid's hundreds of thousands of fans after all these years have been wrong about Samus's character, and we all happened to come to the same false conclusions about her and only now can we all see just how wrong we are.
You see, the thing that gets me about the whole thing, is this whole 'silent loner' thing is pretty much how Samus acts in Other M, externally. What people seem to gloss over is most of the game is
internal. It's Samus narrating past memories, past
bad memories, after going through a traumatic experience. Not to say she's perfectly what you're apparently wanting, but I bet if they stripped away those narrations, and just stuck to the external stuff, most of the complaints would be much lower, because it's really not that far from the character people wanted. But we were going into Samus' head here, and her head was not a Han Solo/Bobba Fett clone.
Not to mention the problems had, the 'whining', the 'dependency issues' aren't nearly as bad they're made out to be. I've seen worse. About the only thing that seems valid is her reaction to Ridley, but eh, even that isn't all
that bad in context.
It's not just a matter of Metroid having grown to be bigger than its creator (or in this case, one of its co-creators)-- obviously, what was present in the past games was enough for fans to come to draw conclusions about the character of Samus, however dark and mysterious she was. She was not a blank slate-- she was more like a sculpture whose details had yet to be defined, but Other M took that sculpture, squashed the clay and then reshaped it into something that looked quite a bit different from what people had seen originally.
No, that's exactly what it is. Want to prove me wrong? Okay, let's start looking at some examples. Where's this 'sculpture' coming from? She's barely spoken at all, barely done anything
at all. Far as I know, the only time we've seen any read signs of characterization is that manga based on Metroid (which apparently matches Other M fairly well, from what I hear, but I know you've dismissed in the past), and I think she talked some in
Zero Mission, but only a small bit. Outside that, she's basically been a walking mannequin ala Link from the previous analogy. So, I guess enlighten me here, where has this 'strong silent type who enjoys solitude and the independence of being a freelancer' come from at all that you can re-enforce from more than 'well, she's silent, and the story tells us she's freelance, so obviously...'?