I disagree with pretty much everything you said but especially on the Shepard point. Commander Shepard has a very strong and well defined personality, that the player can merely guide along a few slightly divergent branches. Shepard always takes part in conversations, always has something to say, always has an opinion to express. I don't think I can recall a single scene (I'm sure there are a couple) in Mass Effect where Shepard stood around listening to exposition without joining in, like Joker does all the time, or only being able to respond to a pointed question with "nod" or "shake head" as was the case in XCX.
So no, Shepard is in fact a great example of how you can write fleshed-out, non-silent characters without completely sacrificing the player's influence over that character. If all silent protagonists were Shepard-like protagonists instead, I would be absolutely delighted. Just imagining Persona 5 with an MC that had that kind of personality excites the crap out of me, maybe then I'd actually care about the character I romance instead of just going with Ann because she was the first girl I came across.