Well the choices definitely don't hold up to close scrutiny. If you look at how the game works and you replay things to try to get your way you realize that you don't actually have that many choices. But if you just play it, they do a very good job of making it seem like your choices directly led to what happens by writing realistic reasons for those things to happen.
Really the only thing that ever bothered me storywise was how Kenneth is totally against you based on one decision. It didn't seem to make sense considering I supported him at every other juncture.