In the article several typical and perspective structures of complex control systems are considered, known and newly developing methods of the optimization of the control of multi-plant multi-criteria systems (MMS) and hierarchical systems are discussed. A new optimization scheme for the two-level hierarchical system of "control-regulation" based on an example of the "guidance-stabilization" system of the aircraft and results of the development of a new algorithm of the equilibrium-arbitrary optimization of the MMS on the basis of the three-channel stabilization system of the aircraft are considered.