I'd say we're in a transition from less rational to more rational.
At the very least we have the capability of empathy so there has been some ratio to this whole morality thing for some time now.
Whatever the reasons for its evolution, it allows us to think of ourselfs as if in the shoes of another. We even anthropomorphize, which brings us into trouble when we project our moral delineators on unsuspecting systems.
And i think that this kind of reflection is realy the basis for any rational moral structure. Reflection being, in a way, a simulation where you analyze the situation from someones viewpoint.
But it somehow seems to me that there is no way to make morality perfecty rational. It will always require a viewpoint and choosing the viewpoint is a moral choice in itself. Is it good, per se, to decide what is good?