All using Morroblivion with All Natural:
Just wanted to check if this is a mod interaction - I almost always get stormy/rainy weather when traveling in Vvardenfell. It is very infrequent that I get overcast, and I have never seen clear skies. My travel has been mostly confined to the areas around Seyda Need, Pelagiad, Balmora, and Caldera.
I use All Natural, but wasn't sure if that even affected the Morrowind world space. Do you guys see this weather too?

Without the weather mod i see
Without the weather mod i see a lot of stormy and overcast weather but only around maybe 40-50% of the time do i see that. Try going to other places eg the most north western region called the grazelands. It tends to be nice weather their or on the island of Solstheim it tends to be snowy or clear skies. But i think it may be a conflict in the mods as when i used Natural Envrionments mod it screwed up the weather on my game it did a similar thing.