The problem with pre-built or non-silent protagonists is that they might not please the person controlling them (I had this issue a lot with FF XII, I empathized A LOT more with the villain then I did with the hero, and in some other games I'd actually enjoy seeing the death animations of "main characters" that I disliked)
I'm not saying that the player should always be avatar himself in the game [ex.: The Super Mario series, I don't feel like I am Mario, but making him (somewhat) silent has helped me play the games more enjoyably and allows me to focus much more in the world surrounding Mario, which is much more interesting then his "blank-slate" persona]
The ideal, for me, would be the impossible! Aka a Custom Character builder with all the possible dialogue choices and all possible voices well acted to perfection (none existent game, basically). But some games get close (Dragon Age, The Sims, Fallout 3, etc.)
I want this in my games because I like to make stories based on the game's theme, I like to build the protagonists for my stories (as if they were my wooden toy puppets) and then I like to follow the story to be close as possible to my desired experience (as in playing with said wooden puppets).
This doesn't mean I don't like pre-built characters, but it does mean that games with pre-built characters and stories are taking a BIG risk when I play them, as I may really dislike them, or really enjoy them [see: Final Fantasy 6 as I loved the story, main cast and especially Villain! Though I can also see that someone the opposite of me would have hated it]