Some of your reasoning for the natures aren't good. A typical fire cannot melt a rock. The current system makes sense and like what PraiseLuka said, your suggestion won't be considered since the nature system is part of the naruto lore . Water can clear a fire out. Wind helps increase a fire's flame. I'm not sure about the link between wind and lightning but it might be about lightning/thunder storms. Lightning literally strikes the "earth". Rocks can stop the flow of water.