A system includes a parameter module that determines at least one of a position of a throttle and a load of an engine. A cylinder status module generates a status signal indicating an activation status of each cylinder of the engine. The cylinder status module determines whether one or more of the cylinders are activated. A first pressure prediction module, when all of the cylinders are activated, predicts first intake port pressures for the cylinders of the engine according to a first model and based on the at least one of the position of the throttle and the engine load. A second pressure prediction module, when one or more of the cylinders is deactivated, predicts second intake port pressures for the deactivated cylinders according to a second model and based on the status signal and the at least one of the position of the throttle and the engine load.