It wasn't really the best example, (SPOILER)the villain was just another evil sadistic type villain, until he at the final battle explains what his motivation is. So you find it out at the very end of the game, while being the goody-two-shoes hero throughout the rest of the story.

Unfortunately, most optional things to 'shape' your character only determine minor things, and not really the outcome of the story. (Ex: Private Actions in SO, I'm sure you know about those), which just determine minor things but don't actually change the entire story.