Well, let's think about it this way-yes, moral choices in gaming ARE usually polarized to the point of absurdity, eg. "Do you want to save this character dying of plague, or kill him, steal his money, and burn down his house(because evil)?", but, even with their flaws, moral systems do add something to the overall experience if executed correctly. I admit, Mass Effect's morality mechanic makes the majority of the ethical dilemmas presented to the player ineffectual, because the Paragon option is usually presented as having some storyline or gameplay benefits, whereas the Renegade option is almost always puppy-kickingly evil and seldom provides benefits to the player other than preemptive elimination of one or two enemies. This is not a well-executed moral system because the benefits(in both story and gameplay) afforded to the player on one side of the spectrum far outweigh those on the opposite side.
But consider, on the other hand, inFamous. It's a fantastic open-world sandbox where your moral choices don't come in the form of dialogue trees, but rather in how you, the player, choose to interact with the world around you. Once again, the choices presented are quite polarized(Do you want to revive the wounded civilian, or drain the lifeforce out of them for giggles?), but at least in this game there are advantages to both sides. If you choose to walk the "Hero" path, you receive special upgrades, exclusive powers, and the adoration of those around you. If, instead, you opt for the "Infamous" path, you receive an entirely different skill set, and the gameplay benefits of the evil path arguably trump those of the good path. Also, in inFamous, you have a reason to want the evil path-more power for you! Ultimately, this morality system is still flawed, but by giving the player more or less even benefits on both sides of the spectrum and an acceptable in-story reason to choose either, it is far better executed.
In short, developers have to give us compelling reasons to play the hero AND the villain, along with some ethically ambiguous, thought-provoking "grey area" choices, to create a truly compelling morality system.