This paper presents a control reconfiguration approach to improve the performance of two classes of dynamical systems. Motivated by recent research on re-engineering cyber-physical systems, we propose a three-step control retrofit procedure. First, we reverse-engineer a dynamical system to dig out an optimization problem it actually solves. Second, we forward-engineer the system by applying a corresponding faster algorithm to solve this optimization problem. Finally, by comparing the original and accelerated dynamics, we obtain the implementation of the redesigned part (the extra dynamics). As a result, the convergence rate/speed or transient behavior of the given system can be improved while the system control structure is maintained. Internet congestion control and distributed proportional-integral (PI) control, as applications in the two different classes of target systems, are used to show the effectiveness of the proposed approach.