Other MI haven't played MOM yet, but from everything I've seen and read it seems the complaints largely boil down to the fact Samus was given a personality. People hate that she's too "girly" (which is just as sexist when it comes from feminists).
"In previous games she was a rock hard bad ass killing machine!"
yeah. . . she also had zero dialogue and could as easily have been a man or a fucking robot. If people don't like her character, fine--people tend to dislike characters like Shinji Ikari and Luke from Tales of the Abyss too--but contrasting her with an incarnation that had NO character is silly.
Sorry, I have to disagree. Samus had a very well demonstrated character. There are many ways to show a character's personality and dialogue is only one of them.
I've played up to Super Metroid only (no Primes =/) and it's still obvious Samus has more balls than I'll ever have.
Samus walking through an empty (that shouldn't be) space station littered with corpses. Pushing on because she needs to confirm what happened to the metroid she captured single-handedly (you know the scariest thing in the galaxy). She then encounters a space pirate mutant and proceeds to gun him down (note that there is zero animation/cutscene about her hesitating or being afraid). After he flees, she hunts him down.