I developed a love for stories by reading books at a young age, and most of the video games I played back then weren't story-based RPGs anyways. So I've never really understood the gimmick of a silent protagonist. Yes, self-projection exists, but I never actually felt like I was Crono in CT. The choices I received were trivial at best, like deciding when to proceed to the final battle or whether to accept a certain seventh character into the party (trivial story-wise, maybe not gameplay-wise).
The problem, also, is that these types or RPGs are often structured where the story is told vicariously through other characters, even though "you" are the protagonist. Like in I am Setsuna, there are character arcs for each character who joins except Endir, the protagonist. It gets to the point where he's just along for the ride. I felt the same way about Crono where even though I was clicking my way through choices, Marle or Lucca were the ones forcing the story along.
Plus, let's remember what we're giving up. A speaking protagonist gives purpose and drive to the game. They develop in ways we can see directly. They're able to develop relationships with other characters. They give substance to the story - another layer to its purpose. Like, Treasure Island could be just a run-of-the-mill novel about pirates and mutiny, but Jim's perspective and his interactions with Captain Silver makes it a tale of adventure, coming-of-age, and true desire. Why miss out on all that?
Personally, I believe silent protagonists will never be more than a gimmicky hindrance to storytelling. To some, it might even encourage laziness since it's one more character you virtually don't have to write.