Part of this is what I've been told, the rest is what I filled in for myself. Therefore, it may be unrepresentative of Christian theology, which I've studied very little of outside what is said by the Bible itself.

>The second view is a hypothetical view that I created only because I was unable to come up with any other explanation for the Christian viewpoint. In this simulation, souls have some sort of intrinsic nature that they can rely on to aid them in their decisions. This intrinsic nature is set by god. Again, though, this removes "true" free will from the souls, since they have no control over the only tools they have for making decisions.

This sounds very much, to me, like the beginning chapters of C.S. Lewis' essay "Miracles." I'm going to only mention selected high points. If you want an extremely careful, high-quality argument, read his essay. It's not long.

The "intrinsic nature" by which humans can make decisions separate from their experiences is rationality. [Or reason, logic, truth, whichever term you prefer.] A rational decision cannot be the product of irrational causes. If a man obviously high on drugs tells you that people are trying to kill him, you'll probably ignore him. If a child tells you that your apple is poisonous because it is red (and no other reason), you'll likewise not be concerned. If we know an idea to be irrational, we discard it. We do not allow that irrationality can compound on itself to become rationality. Perhaps by luck, irrationality may come to a beneficial conclusion, but no one would consider it anything more than dumb luck. One might say that no irrational decision reflects free will, since they can all be accounted for by irrational processes, and that all rational decisions do show free will, because of the following.

There is no room for reason in deterministic physics. If decisions are nothing but the product of chemical reactions, then rationality is a myth. However much the ideologue is tempted to scoff, claiming that logic is limited, there is no way out of the contradiction: if there is no rationality, then one cannot rationally prove that there is no rationality. It's an attempt to prove the invalidity of all proofs. It's nonsense.

Some do not consider this a problem. They willingly surrender the claim that anything they say or write or do is true. They hold, at least when pressed regarding the issue, that there is nothing but utility, as determined by some variant of evolutionary psychology. (Of course, there's a single meme that they can't account for, that being the idea of rationality.)

Most people, however, want to keep rationality in the picture. Where does rationality come from? If humanity were the source, then humans would be entirely rational, which is not the case. There are two possible sources, it seems, of rationality. The first (as Dave has also suggested) is QM. It seems very odd, however, to ascribe rationality to subatomic particles. Will I get in trouble again for stating that rationality is not reducible? That it might be reducible is logically eliminated, because rationality cannot come from irrational causes. The second probable source is God. I'll split from C.S. Lewis here. I see no reason why it couldn't be both, that is, that QM might be the route God uses to get rationality into our heads and free will into the universe.

On the other hand, maybe I misunderstand QM. Are conclusions in QM unknowable beforehand in principle, or only in practice?

And on a different subject: omniscience and free will never contradict, because foreknowledge does not imply control. I know with 100% certainty that those reading this will sit down at some time in the future. I have not just stolen your free will.