Ditch the system part entirely, and rather than just giving us flat-out good and bad options give us more really grey-ish scenarios where the 'right' outcome is potentially whatever the player thinks it is. Mass Effect 2 had a few moments like this (Collector Base, Geth Heretics in particular), unfortunately thanks to the whole moral choice system (ie: make the same choices over and over again or you get a shitty ending) bit, and the fact that all your squadmates rather uncharacteristically pretty much berate you for making the 'wrong' choice afterwards (especially true for the first example), it kind of shoots itself in the foot.
If there is some sort of system tied to it, as in you accumulate points towards a different thing depending on your actions, they should be more tied to how certain groups or individuals perceive those actions.
If there is some sort of system tied to it, as in you accumulate points towards a different thing depending on your actions, they should be more tied to how certain groups or individuals perceive those actions.