An engine control system includes a prediction module that, during an exhaust stroke of a first cylinder of an engine, determines a predicted intake manifold pressure at an end of a next intake stroke of a second cylinder following the first cylinder in a firing order of the cylinders. An air per cylinder (APC) module determines a predicted mass of air that will be trapped within the second cylinder at the end of the next intake stroke of the second cylinder based on the predicted intake manifold pressure. A fueling module controls fueling of the second cylinder during the next intake stroke based on the predicted mass of air.