So games with moral choice systems have been getting better, no longer is the choice to either save the orphan or burn him alive, but it's still got a long way to go.
Take for example the Tenpenny Tower's quest in Fallout 3, where the "good" action is basically acting like a retard, or in the same game the Vampire quest line where you are basically acting like an enforcer running a protection racket. Then there are a number of quests in Mass Effect 2, a game that generally gets the moral choice system pretty right, for example one of the first "found" missions you do via scanning has you finding data that could harm your partners if released to the public.
Of course the good action is to send it to the authorities, the neutral to send it back to them, and the "evil" to keep it for yourself, seems pretty straight forward right? send it to the public to be a good guy, wrong, moral choices very rarely exist in a vacuum, you never forget in the game that you're working with them because it's the only choice, so antagonising them is plain stupid, the good choice should be to keep the data, and the evil choice should be to send it back to them. After all there is nothing stopping you releasing it once you're done with them? Now some people might say that fits the definition of Mass Effect 2's morality system, which defines the actions as moral and ruthless, and keeping the data back is pretty ruthless (I'd personally say intelligent).
But the problem is, in most games with a moral choice system, it's one or the other, you can't be an angel and a demon, and there is no reward for being a well rounded character, and you're punished for taking different actions, for every "evil" action you take, even in games that don't take away from your "good" score like Mass Effect 2, you're punished because you've lost access to those "good" points which can drastically effect the plot, forcing you to make decisions you'd never make in the same situation if it was reality.
You often hear players say "this playthrough I'll be evil" or similar, but is that something we want as gamers? or would it be better to let us play the game as we want? making decisions based on the situation as if we were there, rather then forcing us to conform to a pre-established moral system.