I think it's fine how it is to be honest. But if you seriously want to suggest this thing, then submit it in Customer Service, not here.

Pokemon? xD

You know the element thing is NOT a game thing right? It's actually part of naruto lore?

Lightning beats Earth simply cause it lets the Lightning User go through their Earth Style jutsu's easier. (Generally Mud Walls)

Also it won't change cause that is how it works in Naruto.

To add onto this, one of the most prominent examples of lightning countering earth would be Deidara

Spoilers to Shippuden (Not that it's really unknown)

Deidara was already shown to be skilled, however, Sasuke found his fatal weakness, electricity, which disabled his explosions, which were earth. This pretty much kinda led to Sasuke's victory and Deidara's death. Things would've been a lot easier if Sasuke used just fire.

Later on, Edo Deidara was impaled by Omoi's sword, over in the 4th GNW/SWW (Shinobi World War). Which disabled his ability to go...

BOOM!!!!

(Trust me, I would've put that in comic sans ms if it didn't look like a 2 year old wrote it.)

To add onto that even more, Kakashi had had used his Lightning Blade and struck Kakuzu from behind smashing through his earth style (I guess Skin made out of rocks or something) and managed to kill the Earth Grudge before it was released.

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.