I'm finally finished refining everything I didn't like about Improved Stock Environment 3. Mostly changes to the colors but also touched the clouds and wave mechanics. These changes are available through two optional add-ons that should be installed after Improved Stock Environment v3, enjoy! Here are some screenshots of the mods in-game, the screenshots show the new clouds and realistic colors together.
#1 ISE New Clouds+Waves/#2 ISE Realistic Colors
JSGME Compatible, installation instructions included. #2 ISE Realistic Colors is compatible with TMO and RFB.
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#1 ISE New Clouds+Waves
#2 ISE Realistic Colors
These changes are pretty significant and I could of released another version of ISE but I believe that some people may enjoy the original colors in version 3. Having optional mods gives you more freedom and customization.