A cylinder control system of a vehicle includes a cylinder control module and an air per cylinder (APC) prediction module. The cylinder control module determines a desired cylinder activation/deactivation sequence. The cylinder control module also activates and deactivates valves of cylinders of an engine based on the desired cylinder activation/deactivation sequence. The APC prediction module predicts an amount of air that will be trapped within a next activated cylinder in a firing order of the cylinders based on a cylinder activation/deactivation sequence of the last Q cylinders in the firing order. Q is an integer greater than one.