Muted protagonists are acceptable and perhaps even preffered in games where story doesn't matter. However, it games where story does matter it is STUPID. It is an obvious hiderance to your ability to tell a story and it apparently done this way so you can, as the OP said, for immersion but I never #*@% notice a diffrence.
Half life is supposed to be immersive but I scoff at that. So what if I never leave Gordon's perspective if all there usually ever is to actually immerse me is a bunch of drab shooting action? All this does is leave me unimmersed and wondering why they never expect me to talk. You want me to feel like I'm actually the protagonist? Give me some #%^@ dialoge options so I can make his personality my own! That's something that would actually make a diffrence! Instead we're left with stories that easily could have been improved upon.
Alright, maybe I'm just venting a little bit. Most of the games with silent protagonists I've played had some of the better stories found in gaming (FEAR, Bioshock, The Suffering, Dead Space, and even Half Life). In the former two games having a silent protagonists goes half-way towards making sense the poor history-less bastards.
So in summary I suppose I can't have much of a complaint until I see games with silent protagonists telling sub-par stories by video games standards as blisteringly idiotic as I think the whole idea of silent protagonists is.