The problem with silent protagonists is that hamstrings the storytelling in a huge way. The protagonist can't be an interesting character in of themselves, don't have a personality to get attached to. A lot of scenes have less weight than they could have because the character hardly - if ever - reacts to those events, and reactions are what gives an event weight. The writers also have to try to write a one sided relationship between the protagonist and other characters, where the other characters have to assume what the protagonist is thinking or doing, and if done wrong it can come off as railroady (at which point you mind as well just have a preset protagonist), or very unnatural (which draws attention to the flaws of your setup).
I'd say that the stories of Pokemon Colosseum, and Pokemon Black & White, would have been a lot stronger had the protagonist been able to converse with the antagonists, usually over ideology.
- In Pokemon Colosseum, you play as Wes, a defector from Team Snaggem. Wes had spent years apart of Team Snaggem committing acts of evil, going around with his bros and beating up trainers and robbing them of their beloved Pokemon. Wes was feared, even by his own fellow gang members. Once the Shadow Pokemon experiments began, and the Pokemon Wes stole were being used to straight up assault people (and take over the world for an oppressive regime) did Wes finally have a change of heart, and he blew up his Team's base and went off on a one man crusade against his former comrades. The bulk of the game's dialogue comes from said former comrades, who you are fighting against. It feels very odd that Wes has absolutely nothing to say to them, when doing so could have reinforced the narrative. You could have had Wes inviting his comrades to join them, trying to make them see the error of their ways. Or rebutting those moments where the admins went "we are both the same". It also feels like Wes was supposed to have some sort of relationship with Rui, and trust becomes pretty important in that later on when Nascour dumps the reveal on her that Wes was responsible for everything in the first place, and throws shade on whether she should be blindly trusting him... but Wes just stands there and doesn't say anything.
- In Pokemon Black & White, the player has some pretty important conversations with N and Ghetsis. Having the protagonist character talk could have fleshed out the Hilda/Hilbert-N dynamic, and have fleshed out the moral quandries of the game. Also, this was the first game where there was a focus on the protagonist character's relationship with their friends (Cheren and Bianca) (whereas in previous games, you only bumped into May and Barry every now and then), so you could have improved that. XY is really, really weird, what with Shauna practically giving a love confession to you... but the PC has no characterization whatsoever, so I have no idea what she even saw in him.
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Silent protagonists are fine if they are not heavily connected to the characters of the story. But in the examples of above, you have the devs really trying to have a story where the player character and their relationships to other major characters is very important to the story, and it just doesn't work that well when the protagonist is silent.
So far, I've heard no emphasis on story in Legends, and if there is, we don't know if it will be written so that the protagonist's relationship to other characters will be important. If the game is mostly about the gameplay, not an epic story, a silent protagonist/nondescript customizeable self insert will be fine.