One of the things many people found quite outrageous about Metroid: Other M - beside its general hideousness - was the decision to give Samus Aran, a character who was a silent protagonist in all previous appearances, a voice. Such choices inevitably annoy the fans, who always, always, always oppose any decision to change something they've gotten used to. That's what makes it all the more odd that Other M, a prequel backstory obviously aimed at fans, did so.
Indeed, Samus' controversial throat noises become even more bewildering in that they're so aggressively needless and watery. Most of her dialogue is in her narration which, as I said in the video, does nothing but clarify the plot for idiots, and she rarely says anything of consequence in-game. It seems like it would be childishly simple for a dedicated modding team to delete all her voice files from the game, turning her into the silent protagonist everyone knows and loves without making the story the slightest bit harder to understand. Then they'd only have the terrible plot, hideous controls and overall pointlessness to worry about.
Now, while Metroid: Other M personally offends me on a great many levels, I didn't go into the game feeling that giving Samus a voice was an inherently bad decision. Silent protagonists present an interesting artistic discussion point. They're a phenomenon virtually unique to videogames as a medium, and their precise purpose and necessity is something I've often wondered about. It really comes down to the kind of game you're making.
The first and most basic case of silent protagonist would be in games like Myst and most text adventures; the characters are silent because they are literally supposed to be you, the player, projecting yourself onto the character and manipulating it to reflect your own emotions and decisions. That's a perfectly valid reason and therefore uninteresting to dwell on.
Another main reason for silence is when the game isn't the least bit character-based and has virtually no reliance on dialogue-driven in-game storytelling. Like, say, Gordon Freeman in the original Half-Life, or Daniel from Painkiller. "Wait, didn't Daniel have a voice in Painkiller's cinematics?" I hear you cry. "No," I cry back. "Shut up. Painkiller didn't have cinematics. And if anyone says it did you should stab them in the throat." Keeping in mind the Golden Rule of "show, don't tell," I hold in higher esteem games which create a story without needing dialogue exposition, in which stable I include Metroid Prime, and that's another reason why Other M can choke on owl pellets.
Actually I've just thought of another reason to have a silent protagonist while writing this. In an FPS like, say, Modern Warfare, where the action is intense and you can expect mustachioed generals to be barking instructions in your ear all day, then - unless it's patiently established - it can be difficult to tell if any of the clashing voices drifting through the battlefield belong to you or not, especially if everyone's having a gravelly-voice competition. So, logistically, it might be smarter for your character to keep his mouth shut. A similar problem occurs even if the game occasionally cuts to third person but everyone is wearing expressionless helmets so you can't see their lips moving. This is incidentally a problem I'm having with Halo:Reach.
So those are the scenarios in which it makes sense for a protagonist to be silent. There may be more, but I can say for certain where it doesn't make much sense at all: When the game is character-based, full of fully-voiced non-playable characters, and when a name, personality and reputation has been assigned to the mute. And especially when the game is trying to take itself seriously. Because in a world of rounded characters, silence just makes you seem like a mental deficient or a stubborn, aloof prick.