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We investigate the structural properties, including isomerization, and melting behavior of two-dimensional ion crystals in an RF trap, focusing on the effects of ion temperature and trap potential anisotropy. We identify distinct crystal structures that form under varying trapping conditions and temperatures through experimental observations, molecular dynamics simulations and theoretical analyses. A simple theoretical model predicts the general trend for the melting temperature variation with the trap anisotropy parameter but fails to account for the finer variations of the melting temperature. We find that the melting temperature is lower around the isomer transitions owing to the structural instability around those points. Our experimental and theoretical efforts enhance our understanding of phase transitions in low-dimensional, confined systems, offering insights into the controlled formation of quantum crystals for applications in quantum simulations and many-body physics.