Silent protagonists are by nature silent (hence the title), but there's a such thing as being so silent that the main character, of all people, might as well be a cloud of mist. A player walks right on through it, him, or her without feeling much of a thing.
Shin Megami Tensei Persona 3, for example, did not disappoint when it came to doing what it generally set out to do. A dark atmosphere was felt throughout its world, and despite being limited to a single city one didn't feel constricted. The battle system wasn't too bad, though at times a player could end up praying for the right move from an AI-controlled ally. There was no need for a little extra oomph to make the main aspects of the game complete. The plot was intriguing. It carried a person through the world of Persona 3.
The problem lay in the relationship between game and its main character. One knows that the silent protagonist is silent so that the player can decide his/her personality, but while some major points of the game center on the protagonist, everything else seems to go around him as though he isn't there. Are the other characters really talking to the protagonist? Do they know he's standing next to them? Does he exist in their minds even as they discuss his meager past? In Persona 3 the protagonist is briefly acknowledged as the leader of the group and later (also briefly) the carrier of a plot twist, yet even then the story seems to insert a fact at random before moving right on. It has the equivalent of dropping a bread crumb during a hike through the woods. Does anyone care? Will they do if they happen to notice? What difference would it make if they did or not?
Looking at Persona 3's overall plot, the whole thing could have been carried off neatly without the protagonist, requiring only a few smidges here and there to cover up his absence. Occasionally there would be the question 'Was he even really necessary?'
So it's a relief when its successor gets a general upgrade. Within Shin Megami Tensei Persona 4 traveling from place to place is less of a hassle, party members can be directly controlled (so none of the half-desperate prayers), but more importantly the characters in the game relate more to the protagonist. It's easy to see that the other characters are talking to him, talking about him, and are doing things with him. No longer having events circle around him, no longer hovering, the protagonist is interwoven with the plot.
This guy is definitely there, even if he doesn't technically say a word. Persona 4's protagonist makes it clear he has an existence in the game. Admittedly the Persona 3 protagonist is explained as an orphan, but he has the air of a ghost that died without anybody ever noticing, and then came back to life for the sole purpose of the game. Putting in relatives for the protagonist as done in Persona 4, it gave rise to the feeling that the protagonist didn't come out of thin air, increasing that important character-player connection.
It's nice to know that someone doesn't exist only in one place, or has the air of being unnecessary.