I tried it out with enhanced skycapes, and it worked perfectly. The script just darkens the sim, but only in cloudy weather. When you set clear skies, the sim will be bright again.
I think it's worth a try.
Hi! Go to X-Plane.org, and download cloud art, and then put the cloud art.lua file into flywithlua, scripts folder. the other files don't need to be copied.
Its not perfect, but it gets a lot better.