A. Possible reasons that God does control the weather:
1. An all knowing being must know how to control the weather. Since the weather is there He must be controlling it.
2. It is possible that there are extra dimensions in which the weather can be controlled but we can not tell. It is impossible to have a perfect analysis and perfect atmospheric model in our dimension but perhaps there are other dimensions this can be done from.
3. If God can control any other aspect of our lives then it must be possible that He can control the weather.
4. Since there is existence that we sense, then there is an ultimate reason for this existence (a creator). An entity with that power will have the power to control the weather.
B. Possible reasons that God does not control the weather:
1. Assuming God can only do good, weather such as tornadoes and flash floods can kill and hurt people. If God controls the weather then it would mean He chooses to hurt and kill people and that is bad. It could be though that our souls have entered into a pact for this to happen.
2. If there is not a God then it would be impossible for God to control the weather.
3. Perhaps He chooses not to control the weather. All weather events occur naturally governed by physical laws, quantum mechanics, etc.
C. Possible reasons for God controlling and not controlling the weather both being true:
1. Perhaps God chooses to control some aspects of the weather but not others.
2. Being that God is beyond time and space, perhaps having God control the weather is an illusion. We only think of this type of question since we live in time and space. From God's point of view there is nothing to control. His will is already done.
3. Perhaps God has power to create and destroy the universe but no power of what happens in-between those two events. When the universe was created perhaps the fate of how it would end was determined at that moment also. Since we are between the cusps of creation and destruction things only happen naturally in our current existence.
4. Suppose that God is everything. In this line of thinking it would mean that God is the weather. Since God is the weather, then the power of Him as an outside force having to control it is an illusion. This would also mean that people are part of God and thus people can play God by controlling aspects of the weather (pollution, cloud seeding, etc.).