A new editorial on Bitmob draws attention to the lack of repercussions to many of the choices present in modern role-playing games, though they do at least call out Alpha Protocol, Fallout 2, and Deus Ex as being good examples of choice and consequence done right. An excerpt, as usual:
Many modern designers fall into the trap of choice for the sake of choice, making it meaningful with something that doesn't really change the experience very much. Infamous is a particular egregious example of this, sporting a morality system alongside its open-world gameplay. The extremely binary nature of it is almost a parody of morality systems, but where it really fails is the lack of consequences behind choices. Occasionally, you'll come across an event where you'll be forced to choose between the good choice and the evil choice. And there's no confusion about which is which, as big blue and red icons show exactly what they are. You're morality gauge will merely slide more good or more evil. The only effects to either path are through abilities exclusive to a certain alignment and an ending for each alignment. There aren't really meaningful consequences, as making either choice has no bearing on what happens next in the gameplay most of the time. Rather, choosing one or the other is merely a constant questioning of whether the player wants to play as good or evil. While most games with a binary morality system provide more consequences than Infamous, the end result is often the same: Cause and effect get unbalanced. There's a whole lot of cause with not a lot of effect.
It's not a new enough concept to be excusable, either. Landmark games like the Fallout series and Deus Ex were pioneers of consequence design. Both provided many options for the player, connecting choices with divergent gameplay to create vastly different experiences. Fallout in particular is famous for their ability to be beaten in ten minutes depending on certain choices. Even the character development underpinnings had a tangible effect. Having an extremely low intelligence in both the original and Fallout 2 will cause your character's dialogue options to be extremely limited, most of which is gibberish. This isn't the most ideal way to play the game, but the fact that it's in there at all shows the game's commitment to consequences. Deus Ex also provides this same sensation, programming in multiple different paths depending on your approach. Variables like how characters treat you and even which bosses you fight can really create an experience that is the player's making.