I have to agree that it's dependent on how much of their own character your protagonist is and the circumstances of the story/game.
For example, I'm messing around with a few things right now, and aside from my serious/main project, I have a smaller one where the player is a researcher studying a particular area and periodically reporting back to their lab. In this game, the protagonist speaks normally because it's pretty important to know what they're saying back to their lab/what they've communicated and what they haven't. In, say, the PMD Explorers games, if memory serves, the player repeatedly showed a talking animation and then the NPCs responded as if they explained a given situation, but you never saw what they said; something like that is good enough for a game like the main series games, but in this case, with the player character being alone for much of the time and with no other researchers around to restate specific observations, it's important for the player to be able to see the protagonist's thoughts. In addition, while the player character is the only researcher, there are other characters who aren't researchers, and for the player to be a silent protagonist would rob what is becoming a pretty important juxtaposition between the player's scientific, detailed perspective and the other characters' different views on the setting. Things like this really make it worth having a speaking protagonist - the game won't be out for a long time (it goes hand in hand with my main project, so they're probably going to be released around the same time even if this one is smaller and likely to be finished first), but whenever you finally get a chance to play it, it'll be really easy to see what a different game it would be without the player speaking.
That said, it's really dependent on the story you're trying to tell - for instance, Journey was designed to be silent and made really effective use of that to add to the emotion and exploration; just like the aforementioned project wouldn't be the same without the player talking, Journey would be a much less captivating experience if there was dialogue in it, and it's the silence that makes your solitude so emotional; breaking that by having the player comment on things every ten minutes would be really awkward and rob it of its value. Even the few times when you do meet other characters, all of your interactions remain silent (some important information was conveyed through visions, but never text or speech) and it kept a forlorn, mystical feeling.
Meanwhile, in a project that's focused on a Pokémon Trainer's journey like the official games or my Divide and Unite, it makes sense that you'd want to give the player as much of a blank slate as possible even if there isn't a reason for them to be silent. And even then, other NPCs sometimes react to what the protagonist "said" but didn't say (to let players fill in the blanks of how they might have said it), and the player can have dialogue options that are more interesting or specific than "yes" and "no" (I appreciated how Sun and Moon occasionally gave snarky observations as dialogue options... I feel bad that I can't think of any examples now, ahaha) to make them feel more like you as a character ("would I say x this way or that way?" even beyond just "is the answer x or y?") rather than no character. So there are more ways to handle silent protagonists than just "silent, yes/no, silent" and so on, and some developers might prefer to do that to make the experience fun and engaging while allowing the player to project more rather than be superseded by a preexisting protagonist.
Personally, I don't mind vocal players and generally welcome the protagonist as their character (as long as they're not unspeakably dim), so it's good to remember that even if something is a tradition in the official Pokémon games, it's not sacred and you can reconsider it if it would work better for your game. But I also see the appeal in a silent protagonist where it adds emotional value, or when you're actually meant to be a blank slate; it depends very much on the game and what the developer wants (and, as Luka pointed out... if the developer just prefers to play games with silent protagonists, why wouldn't they make theirs silent? XP), but there are a lot more options and reasons to consider than "Game Freak does x, so x!"
