Traditional autopilot design requires an accurate aerodynamic model and relies on a gain schedule to account for system nonlinearities. This paper presents the control architecture applied to a dynamic model inversion at a single flight condition with an on-line neural network (NN) in order to regulate errors caused by approximate inversion. This eliminates the need for an extensive design process and accurate aerodynamic data. The simulation results using a developed full nonlinear 6 degree of freedom model are presented. This paper also presents the stability evaluation for control systems to which NNs were applied. Although feedback can accommodate uncertainty to meet system performance specifications, uncertainty can also affect the stability of the control system. The importance of robustness has long been recognized and stability margins were developed to quantify it. However, the traditional stability margin techniques based on linear control theory can not be applied to control systems upon which a representative non-linear control method, such as NNs, has been applied. This paper presents an alternative stability margin technique for NNs applied to control systems based on the system responses to an inserted gain multiplier or time delay element.