A system includes a command generator module, a compensation module, and a fraction module. The command generator module generates a first command value and one of activates and deactivates intake and exhaust valves of a first cylinder of an engine based on the first command value. The compensation module generates a compensation value for a second cylinder of the engine based on a response of a model to the first command value. The fraction module determines a target value based on a torque request, the target value corresponding to a fraction of a total number of cylinders of the engine to be activated. The command generator module further: generates a second command value based on the compensation value and a difference between the target value and the first command value; and one of activates and deactivates intake and exhaust valves of the second cylinder based on the second command value.