You know, I realized that some time ago. The problem is that, when a videogame shows a story, it's always simple, naive and black-and-white, unless it's a GTA-style game in which you are the bad guy, in which case it's simple, naive and black-and-grey. And that's the only way to do it, because in videogames stories must take second seat to gameplay and experience, and gameplay and experience are better if the story is a simple 'here are the bad guys, beat them' one. (A game in which you end up utterly and unquestionably losing would end up leaving a bad taste in gamers' mouths... it might become a cult classic, but no one can afford going for cult classic nowadays. Of course, you can do like CoD4 and cheat by having two main guys and having one of them get fucked.)
It just shows more strongly for me that the real 'stories' that videogames should tell are the ones players make themselves. The SHIII experience you describe strikes me as very similar to a roguelike - you're always afraid something will come up and murder you when you're distracted, and when you die, you're dead for good. And of course, there's Dwarf Fortress, in which even if a farming mishap ends up with an entire fortress lost to starvation, that fortress still existed in the world, and you can visit it with a solo adventurer, send a dwarfing squad to reclaim it, find up those artifacts end up on the hands of goblins, etc... My point is that the stories video games should be trying to tell are those that gamers create themselves, be it your submarine finally being sunk but taking two destroyers with it or a beautiful seaside fortress being torn to pieces by a dragon. Much better than "oh no, Helpful Tutorial Character B and Evil Flashback Character C are the same person! Holy fuck!"
