An engine control system for a vehicle, includes a delay and rate limit module, a throttle control module, a phaser control module, and an exhaust gas recirculation (EGR) control module. The delay and rate limit module applies a delay and a rate limit to a first torque request to produce a second torque request. The throttle control module determines a target throttle opening based on the second torque request and selectively adjusts a throttle valve based on the target throttle opening. The phaser control module determines target intake and exhaust phasing values based on the second torque request and selectively adjusts intake and exhaust valve phasers based on the target intake and exhaust phasing values, respectively. The EGR control module determines a target EGR opening based on the first torque request and selectively adjusts an EGR valve based on the target EGR opening.