A method, system and computer-readable medium for controlling a control subsystem of a vehicle. The control subsystem includes at least one propulsion, aerodynamic, or other control effector. The system also includes sensors for sensing vehicle position and motions and operating conditions, a control input device for generating control signals, and a generator for generating desired vehicle forces/moments from the sensed vehicle position and motions and operating conditions, and the generated control input signals based on predefined vehicle compensation and control laws. Also included is a neural network controller for generating control subsystem commands for the at least one propulsion, aerodynamic, or other control effector based on the generated desired forces/moments, wherein said neural network controller was trained based on pregenerated vehicle control distribution data. The neural network controller is also trained to compensate for one or more failed control effectors.