A common complaint amongst games that offer so-called 'moral choices', is that the choices are not only too black and white, but often mawkishly so. It's often a binary decision, do you want to be the good guy or the bad guy?
Take Bioshock, possibly the most egregious example. I love the game, but the choice it offers exemplifies the polarised morals you find in modern gaming. Are you the type of person who kills little girls, or are you the type of person that spares them? Even more infuriating is that ultimately the choice is irrelevant, as you reap the same benefits either way, negating any idea of 'doing what is easy, or what is right'.
Obviously, there are some games that avoid this trap. The Witcher, for all it's flaws, has a system of moral choices that are about as grey as it gets. Do you sell arms the elves, knowing that those arms will be used against your (nominally) fellow humans, or do you send them away empty handed, knowing that you've just extended their oppression?
Fallout 3 largely falls into the Bioshock camp. Do you denotate the bomb, thus destroying Megaton, or do you disarm it, saving the town. Are you Megatron, or Optimus Prime? He-Man or Skeletor? Which is why the most recent DLC - The Pitt - came as something of a surprise. On the surface, it's another easy choice, steal the cure for a degenerative disease that infects the people of the Pitt from their cruel slavemasters.
It's not until you've infiltrated the slavers organisation that the easy choice starts to get a little muddy. The head of the slavers seems to have a vision of a a free zone and regrets the necessity of slaves, and the cure is a living child, a baby in fact, that you must steal from it's parents, probably killing them as you fight your way out.
Do you leave the child where she is, abandoning the slaves to their bondage but potentially allowing something greater to emerge or do you kidnap the child and give her to the slaves, continuing the instability for years to come? We're way past light side and dark side points here, and Fallout 3's karma system has nothing to say on the matter regardless of the choice you make.
This is the sort of thing I'd love to see in games in the future, not black and white, but something much more subtle and nuanced, where the 'right' choice isn't immediately obvious.