Hmmm, this isn't anything to do with Haywire, is it? No worries if it is, I'm just curious as I've literally this moment emailed my own first draft of an article for next issue...
Anyhow, personally I like moral choice systems, PROVIDED THEY'RE DONE WELL. It's like, it won't diminish my enjoyment of a game - a still love both Bioshocks even though the moral choice system is very basic and doesn't serve anything except to maybe give a bit more resource in the game and change the ending very slightly. But I'm both a reader a writer, and I have a natural inclination to exploring morally grey situations. Some of the Halo books (Ghosts of Onyx and Glasslands/The Thursday War, to be exact) are intriguing to me because they explore opposite sides (because of the different writer viewpoints) of the same moral argument (regarding the Spartans). When I write stories I like to create characters who have grey morality rather than black and white, and then explore how that affects them and the people around them and the events occurring. One of my 'good' characters is mildly psychotic and enjoys torturing people, yet is staunchly against things like murder. Another one is happy to bring about war to a whole world yet turns on her boss for committing mass murder and destroying an entire city with an antimatter bomb.
The point is, moral choices can be very interesting tools of storytelling, and I'm an advocate of great storytelling in games (as if there's anyone on the Escapist who isn't). Therefore, moral choices can be used well in games. I unfortunately have yet to see a great game that uses it well, though. We almost always end up with choices that simply add points to swing you one way or the other, and end up at either extreme. Fallout 3 (and I assume New Vegas, although I've not played that one yet) does it better than most, but even then you have arbitrary barriers that when crossed plant you firmly in one of three territories - Good, Neutral, or Evil. The only real effect it then has is on the attitude of some characters to you, certain dialogue choices, and the choice of companions, and all this is easily changed by doing a few good/evil deeds in the Wasteland that take half an hour of playing to achieve. Ultimately, there's no real permanent consequence to your choices. The article I mentioned above is about choice in visual novels, but it all boils down to the same thing - a choice system is only good if the consequences are what matter. It's not the choice itself that's important. The results of the choice are what writers need to think about. That is how you make a well-done moral choice system.