I think most of the negativity around it is more over people's perceptions of who Samus should and shouldn't be based on their own interpretations from the limited characterization of her in previous games, more so then the story itself, that aspect alone seems to have created the most hostility.
It's not an issue of "perception" or "interpretation" when Samus acts completely contrary to the character established in previous games. You want to argue that in the NES and Super NES Metroids that Samus was merely an avatar for the player because modern storytelling conventions weren't common back then? Fine, but it doesn't explain how the Samus in Other M is completely different from the one shown in the Metroid Prime games, which were created with full cutscenes (albeit largely unvoiced). But just like how Sakamoto almost seems to go out of his way to not reference the Western-made and more financially/critically successful Prime games, he likewise also probably didn't want to acknowledge the Samus character solidified by Western developers.
Both Fusion and Zero Mission also IIRC had internal monologue cutscenes and some dialogue, and Samus wasn't anywhere near as whiny and emotionally unstable as she was in Other M. I don't remember reading posts and articles around the release of any of those games from people saying that "that's not Samus", yet that was commonly the case with Other M. Other M's Samus is just very incongruous from her previous depictions, especially when it comes to her dealings with Ridley (which I've extensively detailed in my previous posts on this matter). In fact, the only other Metroid product that apparently has a similar Samus was a Japan-only manga, to which I say "if it's not consistent with the other games, it's not canon."
Samus had little to no personality in the Prime games, they largely referenced the Avatar esque take on her. Other M was really the first game to truly delve into her complexities as a character, and I APPRECIATE that. I've always viewed Other M as a retcon/reimagining of the series, including Samus, to push it beyond the avatar portrayal of Samus.
And of course no one complained about Samus in the Prime games, they hardly even dealt with her character at all. They are fantastic games, but hardly attempted to make her a complex, real, character, in fact they primarily took the easy way out and didn't really touch on who she is at all. Fusion and Other M have been the first real attempts to flesh out, and yes, in some ways, retcon/reimagine Samus as a real character, not a cliche masculinized bounty hunter.
Besides, whether one likes it or not, I get the feeling Sakamoto would not consider the Prime games canon, and frankly he likely has the most control (besides Nintendo themselves) over what is and isn't. I'd argue that the Samus in Fusion, personality wise, is contradictory to the Prime depiction of her. And with Ridley, if the Prime games aren't considered Canon, she would have destroyed Ridley only twice previously. To see him come back a third time would have to be emotionally jarring to say the least. We also have to keep in mind that Sakamoto based her character off of Ripley of the Alien series, and she too experienced post-traumatic stress disorder when she re encountered the alien species again and had to overcome that trauma (like Samus did in Other M).
Anyway, this discussion will keep going around and around, so I'm stepping out of the discussion. I'll just end by saying I am glad Nintendo is giving Samus a personality, and making her more then the typical emotionless hero found in other games. If it contradicts the Prime games, then so be it, because I don't believe they even really tried to make her an emotionally complex character. I want to see the series evolve beyond being all alone and without emotion. If it takes some retconning or eliminating some games from the series canon, then so be it.
I enjoyed Other M, and found it to be a promising new step for the series, even if it has some major flaws in its storytelling, including how Samus was depicted (I do NOT think her characterization was perfect by any means, but I found it much better in this then any other game in the series which felt awfully generic and cliche).
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