I think the problem with Silent Protagonists is that in the vast majority of cases the developers miss the entire point in having a Silent Protagonist to begin with. SPs are intended to be someone the player themselves can be in that world, but then they just railroad the character and thus the player into situations that are ridiculous and often completely avoidable if the player had actual input with little to no control over what they're doing, how they do it, or what they say in the meantime. In short, the player is never really given a chance to project their own personality into the game world. For instance, how many times in the story of a game with an SP do you find some NPC that wants you to do something, then you're given a "choice" between agreeing or refusing, and if you refuse they either ignore you and ask the question again until you agree or just say something like "you said no, but you really mean yes, so let's go?" In other words, with an SP the player is supposed to step into the shoes of a character but they're never actually given the chance to step into the shoes of that character.
This is why I like games like Knights of the Old Republic and Dragon Age Origins so much, since thanks to their dialog choice system they give me the chance to give my own personality to my SP to a certain extent. There are limits of course, but in most cases I can find something to say and do that I probably would have if I were in that situation.