I can only hope that once people calm down a little they'll realize, as I did, that what we are faulting Samus's characterization for is more about flash than substance.
Compare Samus to Naked Snake. Naked Snake's personal story centered around his "mommy" issues regarding the Boss. Snake mopes in MGS3 more than Samus does in OM; he even goes through a total breakdown that Samus never even approaches the level of -- and during it he even has to be saved by a woman, who literally helps carry him. He gets saved countless times by women: How many times did the Boss stop one of her allies from shooting him, or let him go when she could have killed him? How many times did she utterly own him? How many times did Snake keep on screwing up all throughout MGS3, far more than Samus did in Other M? How many times did he feel totally outclassed by the Boss, in a way Samus never felt by Adam? (As I recall, the most Samus ever credited Adam for was keeping a cooler head about life-or-death decisions.)
By contrast, going just by what we actually see happening in their stories, Samus behaves as much if not more badass than Snake. She physically whines less, breaks down less, gets saved less, kicks more ass...
So why the differing treatment? At first I thought it was sexism -- that Samus, being a designated "strong woman", could not be allowed to show weakness. At first. But I now realize that it's even more shallow than that:
It's the pitch of her voice -- too high, we say. It's the inflections in her speech -- too monotone, we say. It's the way she looks -- too young, we say. It's the soliloquies she is not actually speaking to anyone -- too whiny, we say, even though it is we who are prying into her most private thoughts (albeit involuntarily). It's the script, which was left literally translated instead of getting a proper treatment. It's because she overuses the word "Baby". (Seriously? Seriously.)
All ultimately shallow reasons, and totally unfair to attribute to Samus the person.
Now I am not defending Other M in terms of its quality of storytelling, I am only defending Samus as a character. It's still fair to say Other M presents her (unfairly) as whiny, the same way a deceptively edited interview can make anyone look bad, but it is NOT fair to say she actually is whiny, because she most certainly is not. That's all I'm trying to say: It's not her fault.