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In this paper, we investigate optimized adaptive control and trajectory generation for a class of wheeled inverted pendulum (WIP) models of vehicle systems. Aiming at shaping the controlled vehicle dynamics to be of minimized motion tracking errors as well as angular accelerations, we employ the linear quadratic regulation optimization technique to obtain an optimal reference model. Adaptive control has then been developed using variable structure method to ensure the reference model to be exactly matched in a finite-time horizon, even in the presence of various internal and external uncertainties. The minimized yaw and tilt angular accelerations help to enhance the vehicle rider's comfort. In addition, due to the underactuated mechanism of WIP, the vehicle forward velocity dynamics cannot be controlled separately from the pendulum tilt angle dynamics. Inspired by the control strategy of human drivers, who usually manipulate the tilt angle to control the forward velocity, we design a neural-network-based adaptive generator of implicit control trajectory (AGICT) of the tilt angle which indirectly “controls” the forward velocity such that it tracks the desired velocity asymptotically. The stability and optimal tracking performance have been rigorously established by theoretic analysis. In addition, simulation studies have been carried out to demonstrate the efficiency of the developed AGICT and optimized adaptive controller.