This looks awesome !
Some suggestions :
- use (semi-transparent?) white rain drops instead of blue ones. Water isn't blue. This is a misconception. In reality, water reflects the colour of the environment. So the only place where you'll find "blue water" is blue is in swimming pools 
- For lightning strokes, I suggest you to use white instead of yellow, or a very pale yellow, close to white. Then draw this surface with a special blend mode like "add" (not multiply), to change colors while keeping shapes.
- Using semi-transparent dark grey/blue as a surface, in "multiply" mode. Make the transparency vary a bit, to simulte a dark cloudy atmsophere.
@Neovyse: Thanks a lot for the feedback! I have updated the files to add all your suggestions.
-Water and lightnings are now white, and water has more transparency.
-Storms add a dark surface drawn with "multiply" blend mode. Smooth transition when it appears/disappears.
-The "add" blend mode for lightnings make them look great (much better now!).
One of the annoying parts was to make the smooth transition for the darkness surface for storms, because the "multiply" blend mode does not use the alpha channel, which means that using opacity/transparency on the surface was useless.

But I made it in a different way, just by scaling the (r, g, b) coordinates (the color {(255, 255, 255)} seems to be transparent for "multiply" blend mode.)