I pondered about silent protagonists as I replayed Twilight Princess today. Link would not work as a talking character, but he is also not someone you're really supposed to project onto: We see his reaction shots all the time, and he clearly has his own opinions, however predictable. He's not a true projection-plate avatar; his silence is simply a flavor, like Snoopy's.
And as such a flavor, it's not for every character. Link works well silent because he's such an archetypal young hero -- there is absolutely nothing standout about him, or his personality, or his history, so it makes sense that he says nothing, because he'd have nothing interesting to say. He is the stock hero, and we would tire of his lines as quickly as he said them.
Samus, on the other hand, has an interesting and reasonably complex past, so she deserves to have a voice. Maybe not what we got in Other M, but still something more than mere silence.