I'm trying to understand what is the proper way to think about the relationship between God and man.

To try to get some perspective, here are a few examples of relationships where one party has more power than the other from the human world.

• On E2 Public Relations Issues: "If Nate decides he hates the letter "R" and kills every user account with that letter, that's his perogative." (legal, but frowned upon)
• kids on a playground: I'll take my ball and go home (bad sportsmanship)
• Owner of a cow: I own it, so I will kill it and eat it. (legal)
• Owner of a baby cow: I will subject it to a hellish life and then kill it and eat it, since I own it, and it tastes better that way. (legal, disapproved)
• Owner of a dog: I will kill it, since it broke a rule I trained it to follow. (legal)
• Owner of a dog: I will kill it, since I feel like it. (legal, frowned upon)
• Owner of a dog: I will kill it, since it broke a rule I genetically modified it to want to break. (if somone did this, it would probably be counted as torture)
• Policeman: I will enforce the law to the maximum against minorities, but be as relaxed as is legal against whites. (this is the mechanism police use to legally do racial profiling)
• God in the ancient world, according to Christianity: I have the right to kill anyone, since I created them all and they've all sinned. I will pick one group of people and be much less strict to them, but I won't defend anyone else in the world against murder, rape, and torture.
• God in the modern world, according to Christianity: I will send some lucky souls to good families at birth, where they will learn the truth and be exposed to the bible at an early age, but I will send most people on earth to families and countries where they have almost no chance of converting to Christianity.

I realize that the difference between God and man is much greater than the difference between two humans, or the difference between a human and an animal, could ever be, and that he has more power over us than a human could ever have over everything else.

On earth, there is no relationsihp where one person is completely justified in doing whatever it wants to the other. Especially in the case of suffering or depriving someone of something, even if you have that right, it is still usually not considered the best way to behave.

It seems to be different in God's case.

However, here is some speculation: imagine if we create a really good version of SimCity that simulated a universe down to the subatomic level. Then imagine we let this simulation runs until life appears, and evolves into something intelligent. Imagine they invent language, and art, and have feelings, write poetry, and fall in love. They have their own version of everything we do that makes us human. Some of them have started to worship something they call God.
What is the difference between your relationship to them, and the relationship of God to the prehistoric world?
In this situation, would it be ok to kill or torture them arbitrarily?

God as explained by Christianity has total control over the real world, and you have the same level of control over the SimEarth world. I believe that it would be wrong to intentionally torture your little sim-creatures. But if that's wrong, then the way God treats us is also wrong. Therefore, either it's ok to unfairly subject your sim-creatures to torture, there's something wrong with Christian doctrine, or human level AI is impossible.

Tiefling's WU says: "Pi's WU, by the way, remains, despite revision, fundamentally lacking in any understanding of theology or Christian teaching. There is no concept in orthodox Christianity of God 'sending' unborn souls anywhere."

I have a bit of a problem with this - look at Romans 9 verses 15 to 21.:

What then shall we say? Is God unjust? Not at all! For he says to Moses, "I will have mercy on whom I have mercy, and I will have compassion on whom I have compassion." It does not, therefore, depend on man's desire or effort, but on God's mercy. For the Scripture says to Pharaoh: "I raised you up for this very purpose, that I might display my power in you and that my name might be proclaimed in all the earth." Therefore God has mercy on whom he wants to have mercy, and he hardens whom he wants to harden. One of you will say to me: "Then why does God still blame us? For who resists his will?" But who are you, O man, to talk back to God? "Shall what is formed say to him who formed it, 'Why did you make me like this?' Does not the potter have the right to make out of the same lump of clay some pottery for noble purposes and some for common use?

In other words, God hardens people's hearts, but still blames them for doing wrong. When they question the fairness of this, the only defense given is "Who are you, O man, to talk back to God"?

That's a pretty weak justification. If you believe in the possibility of human level AI, then a human could be justified in torturing his sim-creatures in exactly the same way. Yet to me that torture would be wrong.