Most probably it was because the game didn't really reach the casual audience, and in the hardcore community (the one the advertising was aiming for) mouth-to-mouth utterly killed it.
And for good reason, I'm afraid.
It was not a bad game, but it was definitely not on the average "Metroid" quality either.
Samus' character is THE SAME she had before. Anyone who says otherwise hasn't played "Metroid Fusion", nor knows the "expanded universe" (AKA the official manga). Hell, even in "Super Metroid" we have glimpses of her insecurities.
The problem was not in "WHAT", but in "HOW". There is where everything went wrong.
First of all we need to clarify something: Team Ninja DID NOT write Samus' character. Sakamoto did. And it was jarringly obvious that he doesn't know the first thing about good characterization.
Making her banging her head over her insecurities over and over... and over, and over, and over... and over (a mistake that bad japanese writers seem to make every time), doesn't make her a likable character: it makes her annoying.
In "Metroid Fusion" Samus talks about her insecurities too, but since she only does it from time to time, and in the RIGHT moments, that made her more human.
The same could be said about every other story issue the game had. It was not a matter of giving a "Metroid" game a heavy story. It was a matter of HOW that story was executed.
And gameplay wise, yes, it was a matter of bad calls and sticking to them out of sheer stubbornness. You want to make a "Metroid" game with retro-feeling gameplay in a NES way? Fine by me. But when you do it with controls like MoM... YOU'RE DOING IT WRONG!
Finally, I feel sorry for Team Ninja too.
Despite their obsession with big boobs (which makes some people to unfairly underrate them), they are a great team. "Dead or Alive" is a great fighting series and "Ninja Gaiden Black" is still the best 3D hack'n slash ever.
But with this game they are receiving some harsh criticism about things that are NOT their fault. The only thing that they truly deserve to be blamed for is the uninspiring level and character design. Not that those are minor issues, specially the first one, but the REAL game brakers (story and control decisions) were not their fault.