from the games i've played, i think dragon age has had the best morality system. It doesn't just say your "good", or your "evil". It makes you think about those choices, and about how your party members and other people/places will reaction to you or your decision. If you make a choice that one party member thinks it particularly evil, they may just up and leave, or even attack you. That for me made the morality system excellent, and much deeper
grungehead1991's comments