For instance, if you don't take ANY revenge whatsoever at the party and then are caught trying to escape Cole, Nathan will still give the same response of "Don't you remember what happened at Kirsten's birthday party? You know what Aiden can do, right? Right?!" That doesn't make sense if you didn't have your revenge.
Also, nothing is explained. If you take the choice and have a guard commit suicide and fail the mission at the fancy Shiek party, it won't affect anything later on.
Same with the amount of times you can reject Ryan. If you reject him at all times, the game still forces you to kiss him when you're about to destroy the condenser.
Also, the fact that you HAVE to save the little kid Salim, and you have to use his Dad to kill the soldiers, it doesn't give you any choice.
When those rapists ask if you wanna play pool with them and if you select "No", the game will still force you to go along with it.
Also, when Nathan asks you to talk to his dead wife and daughter, if you select "No", the game still forces you to go along with it.