A torque requesting module generates a torque request for an engine based on driver input. A model predictive control (MPC) module: identifies sets of possible target values based on the torque request, each of the sets of possible target values including target effective throttle area percentage; determines predicted operating parameters for the sets of possible target values, respectively; determines cost values for the sets of possible target values, respectively; selects one of the sets of possible target values based on the cost values; and sets target values based on the possible target values of the selected one of the sets, respectively, the target values including a target pressure ratio across the throttle valve. A target area module determines a target opening area of the throttle valve based on the target effective throttle area percentage ratio. A throttle actuator module controls the throttle valve based on the target opening.