A novel numerical methodology has been developed, which makes possible to optimize arbitrary emitting dipole and plasmonic nano-resonator configuration with an arbitrary objective function. By selecting quantum efficiency as the objective function that has to be maximized at preselected Purcell factor criteria, optimization of plasmonic nanorod based configurations has been realized to enhance fluorescence of NV and SiV color centers in diamond. Gold and silver nanorod based configurations have been optimized to enhance excitation and emission separately, as well as both processes simultaneously, and the underlying nanophotonical phenomena have been inspected comparatively. It has been shown that considerable excitation enhancement is achieved by silver nanorods, while nanorods made of both metals are appropriate to enhance emission. More significant improvement can be achieved via silver nanorods at both wavelengths of both color centers. It has been proven that theoretical limits originating from metal dielectric properties can be approached by simultaneous optimization, which results in configurations determined by preferences corresponding to the emission. Larger emission enhancement is achieved via both metals in case of SiV center compared to the NV center. Gold and silver nanorod based configurations making possible to improve SiV centers quantum efficiency by factors of 1.18 and 5.25 are proposed, which have potential applications in quantum information processing.