I think game designes are afraid of using that approach because they think gamers will not like it. To be honest, as I was reading the article I thought that would be its approach as well. 'There's this guy called Rodriguez. He's saying he knows me. What the fuck? I just met him, I don't know who he is, and I would never have become friends with a guy this annoying in the first place. Fuck off, Rodriguez.'
Partly it's one of everyone's main complaints on gaming - they have bad stories. People complain that games don't know how to portray minorities, don't know how to portray women, don't know how to be subtle. And they're all true, but that's all because of a simple thing - they don't know how to set up stories. Characters, particualarly, are very difficult to set up in an enjoyable and interesting way. So in the same way games have to turn to cheap tricks like HUEG plot twists in their narratives they have to turn to simplistic stereotypes to use as their characters. Writing it the Indiana Jones way, as you suggested, is hard work. You have to deliver this in a way that the viewers/players care about what is going on even before they have had time to acquaint themselves with the characters and their relationship. This isn't particularly hard - Indiana Jones is not exactly known for its riveting emotional story - but video game writing just isn't up to par.
Partly it's because of the emphasis modern day games have on 'you are your character, your every action molds your story!' MovieBob complained about it just last week, and he has kind of a point. If you can create a character to be however you like and you want him to be a cynical loner, then knowing that you have an old friend who ate pies with you when you were growing up might spoil the image you have built in your mind. It's too bad that the modern industry seems to think this is what they should aspire to, when it's just another approach, both being just as valid.
And of course partly it's because of what I call the 'Outsider Theory', or the full name, 'The Random One's Outsider Theory by The Random One' (pat.pen.). Under that theory, game characters are often outsiders, foreigners or otherwise ignorant of the gameworld because that's the state the player finds herself in when booting up the game. Since the player will be meeting the world for the first time, the strangeness inherent to the game as you're picking up the controls will match the character's strangeness as he learns how things work in the new world. And of course since you have no prior 'luggage' you're allowed to behave in the world as you see fit. Look around and see how many games go out of the way to estabilish a character that is disconnected to the world and is discovering it in tandem with the player. But, of course, this doesn't mean friendships aren't possible. Your example of Fallout 3 points to this - a vault-born in the Fallout world has a great excuse to be an outsider in the wastelands, but she does have family and associates. Nico Belic is a foreigner who knows nothing of Liberty city, but he does have a cousin. You can have your cake and eat it too.