So I made a game, Fading Hearts, with a small indie team that theorically answers the issues of the player changing the story in games. Not small changes but major ones where the end games sometime vary drastically as well as the endings. With everyone talking about how they want more control of the storyline, it leads me to think about why the bigger budget games do not have enough of it.
I guess for now I'll go over what I've learned from making it. This list is a bit more practical than theorical when compared to the stuff I normally read about writing stories in games.
1. The player must be given at least an okay story no matter what they do (should they reach an ending)
2. The forces of plot should try to control the player
3. The player must be able to resist or overturn the forces of plot but must fight for it
4. Two known ways the player can do this either through skill or knowledge of the plot
5. When focus/play-testing you will probably have to write more for weird but theorically possible cases
6. Try to figure out where the player would more likely go and plant clues thereto other plotlines
7. Figure out a way for the story to continue without the player
8. Write-out possiblities in the story that would make your development time explode
9. Keep an eye on the combinatorics of the plots you are writing (not the theroical combinatorics of what the player can do)
10. Stories as games are fundementally mysteries as you are usually trying to find out more about the story
11. You have to start with the story very very early.
There is probably a bunch more I forgot. I can probably only recall half at one time. But tell me what you think about this list.