Firstly, remove the system as a whole. As others have mentioned, Morality systems tend to be built around the idea of players making choices that come out in one of two ways. Developers than tie into that system certian rewards and such for getting to a certian level of good or bad karma. Like Mass Effects Paragon/Renegade choices. To get the best outcomes in some places, you had to choose mostly paragon or renegade options in order to activate the option. Instead of trying to roleplay, players now have to play their Shepard as either a saint or a dick.
So my plan is to remove the system. Make all the moral choices in game not add up. But that said, have the choices still hold some meaning in the world. A possible scenerio: You come across a young woman being manhandled by a pair of bandits. You could either:
- Save her from the bandits.
- Join in with the bandits.
- Kill her.
- Not do anything.
-and some others...
Having no overall moral choice system, these choices arent tracked as either good or evil, but they will style have some effect on the game world:
- The girl ends up being the daughter of a powerful lord in the region, and he rewards you for saving her.
- Same as above, and because you helped rape her, he now wants your head on a pike.
- Same as above, but with her dead, the lord now wants information to who killed her.
- Same as above, but you simply find out this information (unless she saw you not help her, than she may want you dead.)
My idea is to basically emphizise the choices a player has, and what they can do to affect the game world, yet not have a arbitary system in place to determine whether the action is good or evil, and thus give out a arbitary reward that would make players choose the more obvious good or evil choices for said reward.