Valve control systems and methods for cylinder deactivation and activation transitions

An engine control system for a vehicle includes an air control module and a valve control module. The air control module determines a desired mass of air per cylinder (APC) based on a torque request and selectively increases the desired APC in response to a command to deactivate N cylinders of an engine. The valve control module disables intake and exhaust valves of the N cylinders of the engine in response to the command, determines intake and exhaust valve timing based on the desired APC, and controls camless intake and exhaust valve actuators of M other cylinders based on the intake and exhaust valve timing, respectively. The engine includes Q cylinders, M and N are integers greater than zero, and M plus N equals Q.