I suppose what I'm trying to say is that there's the part of the story they wanted us to feel was the most important element, and then there's the one that functioned anyway regardless of authorial intent. It's like there can be two stories in a video game. The one that plays in cutscenes, and the story that adds up as you play the game. The most "honest to medium" video game stories utilize both into the same package. For example, I think few stories are as truthful to video games as ICO, because the story and the game are so innately intertwined. Two kids learn how to hold hands and care about each other's lives.
By playing a game, the set of actions you use creates the living story.
So if the Starchild, who you can't actually refute, tells you that oh yeah synethetics are gonna wipe out organics no matter what, but in gameplay you just told the story of overcoming that conflict, and both Geth and Quarians are still around...
Interaction is gonna trump exposition, every time. Maybe that's what we need to learn in video games, right? If you're gonna tell a differently toned story than the players are going to create-via-interaction, you're already making fundamental mistakes.
I hear ya.