Honestly; I'm playing through Black/White now and there are quite a few scenes where, in most cases, a person would talk; particularly as the Team Plasma storyline escalates. However, the silent protagonist...it doesn't feel weird, because that's a player-character. It's a video-game representation of yourself, not some story-designated character you might role-play as. There's quite a difference, really. It sort of lets you mold other people's personalities better, because you don't have a person (ie. you) butting in and stopping someone going where they were going to go.
In the end, it's your choice. In my opinion, though, if a game lets you name the main character, then the protagonist should usually remain silent (eg. Pokemon). If not, then it should be fine (eg. Final Fantasy). There are games with the opposite (eg. Mario and Luigi has the titular character not really talk, and FFTA2 has your "player-character", talk), so, really, it's all about execution.