I'm not going to deny it, I find moral choices in video games fascinating. On the one hand, having options and therefore the illusion of control is very nice. On the other, for fucks sake video games, why is the choice always to be either Jesus, Satan or apathetic?
Our sense of "Morality" is just an avoidance of the negative consequences of actions, a moral system in games needs to be designed to reflect that because games have no real consequences anyway, which is why games have to dangle some form of engineered carrot in front of players to guide their "moral" judgements.
Star Wars: KoToR had simple carrots, dark side powers which hurt enemies and light side which healed and buffed allies. Being light side or dark side was basically a playing style choice. Dark side sometimes had an extra money carrot, but not always. Sometimes you got more from light side.
Mass Effect has two carrots: Being a bastard gives you renegade and lets you do more intimidation, being a paragon let's you be more charismatic. But the carrots are the same both ways, being renegade is just funnier to watch most of the time. I can't be the only player he basically did all the big paragon choices but at every other step of the way was a complete bastard, just so he could laugh at the bastardry.
Both these carrots give players "the weaknesses of amorality", being a grey made you inherently weaker which sucked.
Personally I'd like to see a game implement a morality system akin to that of the World of Darkness: One-way. Being cruel cost you morality, but when only your current morality was above the level of cruelty of that action. A common thief would not lose any more morality from stealing, but if they ever kill someone they'd take a plunge. Also it means the game can easily keep track of how to treat the player, you can't "puppy-poke" your way to becoming the Lord of the Sith.
Of course some kinds of carrots would be required. WoD implements "derangements", as your character goes more (a/im)moral they go insane(r). This means players have to balance the rewards of their "evil" actions with the rewards of such actions.
Such games would also find it easier to gauge NPC reactions to the player. Full morality is a saint who has never took a life (not even in self-defence), middle morality may be a common thief out for himself, no morality a complete psychopathic monster who has definitely murdered their way to that state. It'd be surprisingly easy to track =)