FC5 also has the option to finish the game in a couple of minutes if you do what the antagonist asks. Don't remember what exactly it was, leave with your team, I believe.
FC6 too. In the beginning you're only helping the resistance so they'll give you a boat to escape to Miami. Once they give you the boat you're supposed to join them anyway, but if you take the boat and sail far enough away you'll get a cutscene where you escape to Miami and later watch the fall of your country on the news.