Who did it better, Pokémon Logic or Monster Hunter Logic?
In terms of fire attacking water entities, I think water should not be resistant to fire; in fact water should be weak against fire. Take Monster hunter's logic for example. Water monster's hides are used for adaptation in the water. This is why their bodies are soft and streamlined so that they can resist the current flow of water. They need moisture to survive and because of this they are not prepared for the heat, their skins are not made to handle fire.
The reason to why fire is weak to water is that water suffocates fire by depriving it of oxygen. And this is why fires are extinguished by water. You can put fire above of water and it will still burn.
To adapt to heat and fire, hides and skins must be rigid and hard. This is why monsters like diablos and uragaan are resistant to fire because their bodies are hardened to resist heat.
If Pokémon truly wants to follow logic, they would make ground types to be resistant to fire and water to be neutral of even weak to fire moves.