I've never had problems with silent protagonists, it may have to do with the fact that I can list more bad character protagonists who sunk a game than a silent one that did. It usually depends on the type of story as well because when you think about it, not all main protagonists are really the main character of their tales, so if the plot is going to focus more on secondary characters anyway, having a playable protagonist that can emote a little bit is often just as good as one who has actual dialogue.

I remember people being annoyed with Xenoblade Chronicles X for having a silent protagonist, but when I really think about it, I actually felt like Shulk would have been more likable as one in Xenoblade itself because he's honestly the most boring member of the cast despite the twists that connect him to the plot. Star Ocean would also work out better if the MC's were silent heroes as they're often the most unlikable members of the team.

Likewise, I've generally always liked the main protagonists of a Persona game despite all of them being silent protagonists, and I feel the impact of those games would have been diminished a bit had they become talking characters, in fact the largest valid complaint against P2: Eternal Punishment is switching around two characters from Innocent Sin as the silent hero and talking support character. Most fans agree Tatsuya was far more likable when he didn't talk, whereas others missed having chatty Maya suddenly become comically stoic.

As for best examples, I'll simply echo what's been said. Persona, Shin Megami Tensei, Suikoden, Breath of Fire, and the Chrono series are all good examples of a silent protagonist working. Whether it's because the characters emote well like Ryu or Chrono/Serge; the game giving you wonderful flavor text choices to really give identity to them like Persona, Mass Effect, and Suikoden; or if the premise of the story really falls into making the player actually feel like the MC and their choices matter such as Shin Megami Tensei.