Morality systems in video games fall under scrutiny for being stark and overtly binary in the eyes of certain gamers. The absence of a grey choice, in a metaphorical sense, is what I perceive to be the issue people take. That, as well as the tendency to justify moral choices in an arbitrary fashion, with little rationalizing to determine which path you should take, apart from personal preference. Morality itself is defined as "actions that mark the distinction between right and wrong and good and bad behaviors", and in video-games morality systems are implemented as such.  They lean towards the separation of good and evil by meters and measures, and often enough the choices leading to those ends are as polar as positive and negative.  The state of the industry is therefore more reminiscent of the philosophical leanings of Immanuel Kant, and the counter arguments to his ideas, as far ethics are concerned.

Immanuel Kant believed in an absolute form of ethical boundaries known as the categorical imperative.  This line of reasoning stated that in any given circumstance moral boundaries are absolute.  This was an offshoot of Deontology which is centered around the idea that actions and the people committing them are separate entities in and of themselves.  That is to say following an action through to get to an end, ergo: the ends justify the means, is a morally unscrupulous act.  The imperative of Kant was to suggest that people themselves are ends and not means.  If you stole a loaf of bread to feed your starving family: You are in the wrong.  In a broader sense the Categorical Imperative can be summed up by asking yourself a question: How would I feel if this was world-wide?  For example; it is wrong to lie about your credentials when searching for a job because the world in which everybody does that is not an ideal one.  From Kant's point of view you had to act as the supreme moral conscious of the world in order to stay ethically right.

Kant's works existed in contrast to another ethical guideline, that of Consequentialism.  Consequentialism viewed people as means to an end, or to say that the ends justify the means. Consequentialsits believed in the universality of good and evil.   Killing a man, or stealing bread to save your family is okay by consequentialist guidelines.  In a phrase Consequentialism can be defined as doing the greatest good for the greatest amount.  But of course this is a highly subjective view on moral allegiance.  Bad guys probably think they're doing good, and under that reasoning it's just as easy to say the same about the good guys.

Pertaining to video-games pieces of Kant's ideology and consequentialism can be seen in the framework of ethical guidelines in the morality systems.  Most notably, in my opinion, is that of Fallout 3.  In Fallout 3 it is absolutely wrong for you to steal from what is considered to be a morally upstanding character.  Regardless of whether or not you need said supplies to survive the fact of the matter is what you did was wrong.  In a world as polluted with ambiguity as it is radiation; the consequences of actions remaining independent of your character remain stark.  You can be a neutral character but that in no way changes the fact that you have been doing two things that affect morality: Something good or something bad. 

Consequentialism in ethics is not so much a governance of morality, such as in Fallout 3, but instead as a character description.  The shining example of this in video-games is the Mass Effect series.  As opposed to non-narrative driven Role playing games Mass Effect is centered on how you achieve a required goal.  Along the entire narrative structure you always work to an end, and the choices pertaining to morality are all about the means to that end.  In the Mass Effect series, you are doing good.  There has never been a question of that in the series, but I love how it's up to you to determine how you reach the conclusion of what's best.

As the design philosophy of the RPG genre bleeds more and more into more conventional types of games, ideas and systems continue to integrate into games where you wouldn't expect them.  A narrative heavy Rockstar title, for example.  Or even Call of Duty to an extent, one type of moral choice can be seen in many games we play, and as they develop more they become more elegant and refined, but for now I'm content with what we have in place.  It may be stark, but it makes you think.