Thinman, regarding your subject line: the idea that rationality rests on arational assumptions has nothing to do with Godel's Incompleteness Theorem. A lot of people seem to get confused about this. The Incompleteness Theorem actually states that the consistencyof the axioms (e.g. arational assumptions) of a logical system among themselves cannot be explained within the confines of that system. In other words, you can't prove that the axioms in a system don't conflict with one another (or do conflict with one another) within the confines of the system itself. The fact that these axioms are simply assumptions is taken for granted.
As to what you said about some "moral systems" being better than others, I'd agree, but what you call "moral systems" I'd call "moral approaches". This still doesn't solve the fundamental problem of the inability to reconcile two moral systems with fundamentally different goals. In other words, if I decided today that I'd rather go around murdering people, and made that my top priority, regardless of other consequences (such as jailtime or death), there's no objectively transcendent way that my actions would be "wrong".
Practically, this doesn't matter. Though I don't think the actions of, say, Hitler, were transcendentally wrong (or transcendentally right), those actions would interfere with my personal goals (which include the peace and well-being of all mankind), and thus I would have tried to stop Hitler from doing what he did.
Luckily, human beings tend to have the same general goals (whether they believe these goals to have been created by their self interest, their sympathy for others, or whatever), or else there'd be total anarchy. But then, this would be true even if some kind of transcendental moral law existed.
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