As My GM can attest, one of my favorite things about role playing is using it as a construct to explore ethical and moral issues.
I believe Gary Gygax's alignment system is one of his more brilliant innovations. It can act as a sort of lens through which you can view those issues, and allows you to develop a shorthand personality for your character - the skeleton that you build outwards from. If you know how your character views the world, you can guess how they would react to a certain situation, you can start getting a feel for who they are, and the character becomes more real, with their motivations becoming more intuitive as you go.
There are problems with it, though.
First, it can breed lazy players and GMs. Instead of developing personalities for their characters, they can let their alignments dictate their actions without bothering to come up with motivations - the evil archmage is trying to take over the world. Why? Because he's Chaotic Evil, and that's what Chaotic Evil people do. The Paladin is trying to take him down because he's Lawful Good, and that's what Lawful Good people do. Blerg. I want meat on the bone, I want to know what drives them. I don't need to know they were spanked too many times as a child, but I don't want mustache twirling villains and square jawed heroes either - give me nuance.
Second, it can dumb down the storytelling aspect of the game. Real people's actions aren't consistent enough to fall into an alignment. People do good things one day, then bad things the next. Hitler loved his dogs, JFK was a philanderer, so on and so forth.
Finally, you are ostensibly heroes (assuming you are playing good aligned characters), but if you look too hard at things, the moral righteousness of what you're doing starts to fray around the edges. I played a Dragonborn Avenger in a 4e campaign a couple of years ago, who had a puritanical zeal to convert the world to Bahamut, one bashed skull at a time. So long as I was killing in the name of Bahamut, all was well. Then I got the Command spell, and I decided to actually start taking the "saving of souls" seriously, and things got... uncomfortable.
Kidnapping a kobold, I determined to convert him to Bahamut by a process of behavior modification. With a liberal use of Command, I wanted to get him to "see the light", so to speak. The DM ruled that my actions were leading the Dragonborn away from his alignment and towards evil. Which really, it makes sense, I get it.
But it exposed one of the core flaws in the Alignment system - by depriving the kobold of its free will, I was acting in an evil fashion. Had I simply killed the kobold, however, and deprived it of its will altogether, I would have been acting fully within the boundaries of my alignment.
So as I'm designing From the Ashes, I'm trying to do something different - rather than a fixed alignment, create more of a sliding scale, where your personal morality slowly calcifies over time, your actions determining your alignment, rather than vice versa. Just like in life, you start tabula rasa, and over time, find out who you are. I'm sure Stalin's parents loved him, and Ghandi lied to his mother every once in awhile - it wasn't until they had time to explore their worlds that they truly became who we know them to be now.
Further, I want your actions to be reflected on the world. This is a brand new world, babe, and everything you do will have consequences. As humanity digs itself out of the rubble, it looks to its champions and its villains to identify it, to form their own shorthand for morality. So if you act in a morally upstanding manner, help those in need and do your part to create a better world, your example will lead others, but if you act selfishly and put your boot on the neck of your fellow man, they will do the same to others.
I have a vague notion of some sort of modifier to reaction rolls and increased or decreased chances of random encounters based on where you fall on the morality scale, but nothing concrete as of yet.
That leads me back to one of my problems that I mentioned above, though - how to judge the morality of individual actions - is killing the kobold a good or evil act? I don't think there are any easy answers, but my hope is that the system that I hang on this concept can at least inspire some conversation, some debate, and get people who play it to question and discuss one of the accepted core concepts of role playing - that killing is good.