Yeah, I feel there could be more done with choice and consequence gameplay wise, and there is definitely some smoke and mirrors going on when it comes to story and Alters. Two mandatory alters get easily the most narrative stuff, and out of other optional one one opened some major story opportunities and others seemed rather modest in content.
Looking back at potential story choices and their outcomes there seem to be mostly better and worse options - which I think would be far less compelling on 2nd playthrough.