Okay, I didn't read all the posts here, but I want to add my two cents on the subject of moral choices in gaming.
I actually did a blog on this very subject not too long ago. Here is a copy and paste of it:
(Disclaimer: I personally love every game I'm about to rag on about. I just wanted to get that out of the way before the fanboys come in, read it, and then submit a 45 page essay flaming me about why my opinion is stupid, invalid, and wrong.)
Unless you have been living under a rock for the past decade, or you just plain aren't a gamer (In which case, why are you here reading this?) then you may have noticed that "moral choices" are the next big thing in gaming. This is especially true for RPGs. From Bioshock to Jade Empire, KOTOR to The Witcher, you can probably name fifteen games from the past five years or the near future that use this "moral choices" mechanic easily enough. But there is something missing. What is it, you ask?
Most of these games take a very, very simplistic approach to the mechanic.
There are a number of things that I have to complain about in regards to the way most games approach moral choices. As someone I know once so wisely put it, "Moral choices in general are pretty far-fetched and unrealistic. In real life, you won't stop for a second to consider if you should save a child drowning in the river, so why do games approach it in such a way?" In a way, I agree, but for different reasons.
For one, most games give you entirely too simple choices. They are extremely black and white. You are either good or evil. Take Bioshock, for example. In Bioshock you don't even have a "neutral" choice like you do in Mass Effect or Jade Empire. Bioshock is the perfect example of a very black and white game in regards to moral choices: You are either a Saint of Christ, or a Satanic baby-eater. There is no "middle" ground. Worse yet, in most games the "evil" choices aren't really evil. In games like Jade Empire, being "evil" means being a certified jerk-off. You aren't "evil;" you are little more than an arrogant thug, like the "gangstas" you might meet in a shady part of town.
This often extends to an arbitrary meter that shows how good or evil I am. In games like Mass Effect, you will often find yourself choosing certain choices just to move the meter. In which case it isn't choices made because of morality, it is choices made to push the meter further in one direction or the other. You are letting the meter dictate your personal beliefs in the game.
The most damning complaint I have with moral choices are that, often times, the choices have little impact. In Mass Effect, your moral choices usually only have one, instant effect: The meter moves closer to Paragon or Renegade. In most of these games, your choices rarely have lasting side effects beyond moving the said arbitrary meter. You get your "Light Side/Dark Side points" and some other reward and move along, never looking back. Then, depending on some final moral choice, you get one of several different endings.
One of the few recent examples of a game that I think did the moral choices mechanic right is The Witcher. In The Witcher, your choices aren't so black and white, and your choices often have a consequence further down the road. Example: One of my choices in the first chapter had a consequence many hours later, in about the middle of chapter 2. Likewise, the choices are shades of gray, not outright good or evil as in many similar games. And finally, it doesn't have some meter tracking how good or evil you are.
The upcoming game Alpha Protocol promises a similar approach. The game promises that your actions will have consequences later on, and your choices aren't "good, neutral, or evil." Instead, you pick your "tone" in conversations. The game used three famous agents from pop culture to model these tones: Jason Bourne, James Bond, and Jack Bauer. This means your tone choices are "Professional" (Jason), "Suave" (James), or "Aggressive" (Jack). You aren't good, neutral, or evil.
More games need to take this approach. The "moral choices" game mechanic has a lot of potential. Potential that is often wasted by simplistic "good or evil" ideas and a lack of real consequences for your actions. More games need to shy away from BioWare's typical good or evil approach and look towards The Witcher's shades of gray theme, as well as include consequences for your actions. While we are at it, do away with the arbitrary meter showing me how good or evil I am.
In other words, make it more realistic and less simplistic.