None of these people are ugly, frankly. Well, except for the obvious jokes/goofs. People are only comparing them to what they think is ugly. It's extremely relative to the situation, who these people are, and where they are, etc.
Also John Marston isn't ugly, he's got scars, huge difference. Male Shepard is modeled after a real male super model, so it's pretty funny that some people call him ugly, lol.
In my opinion, almost all character models in the Hitman series take the cake. Especially the latest entry, and the mission with the porn models. That's the kind of ugly that everyone loves to hate. The unnatural, plastic enhanced, fake appearance loaded with unknown and disturbing features. Most of the models look very strange, and intentionally done to make everyone appear like that kind of "snobby fake", that's immediately apparent upon looking at certain people.