This sort of thing REALLY bothers my sisters because I think, unlike me, they are visual storytellers. Since I write novels, I don't care too much about designs; writers don't really describe their characters too much physically most of the time so I feel designs are less important to them most of the time and most writers wouldn't be bothered by characters having the same faces. However, I do definitely think it adds something if the characters have different faces in a visual medium. I guess it's a case where I'm not bothered too much if all the characters have the same face, but I prefer if they don't.
One of my favorite mangas/comics ever is Akira and it's both for the story and art style. Kaneda and Tetsuo have different face shapes, but not only that, the brilliant artist, Otomo, was never afraid to make his characters look ugly or unappealing. It's a dark, gritty story and Tetsuo--however much I might pity him--is an ugly human being and Otomo was never afraid to show that despite the fact that Tetsuo isn't exactly the worst looking kiddo out there.
So I think something even a little bit more important than design and different face shapes is just HOW the characters are drawn. The last picture from Akira I threw up here has gotta be one of my favorite pictures ever, and while designs do play a part in that, it's the lines, the lighting, the posture of the characters, and the details that make it so stunning in my opinion.
Like, even without reading the story, Otomo captured a moment in that last picture where visually someone can glean what's happening between the characters and that, I think, is a special thing.