Thing is, as well, it's one of those things where I (personally) wouldn't be fussed about seeing precisely the same weather as somebody else as long as we both experienced the same type of weather.
Obviously, a PvPer, for example, might think it's a serious issue if they were, for example, trying to head into a cloud for cover when they have no way of knowing if their opponent is going to see the same cloud but, meh.
In that case, I guess the answer is to not rely on weather attributes for cover.
Seems like it would be possible to come up with a simplistic model to generate "bubbles" of dynamic weather on a planet's surface based on stuff like temperature and geography.
You fly into, say, a "heavy rain area" and you get droplets on your canopy, there's reduced visibility of distant objects and, perhaps, you get flickering on your HUDs, sensor problems and engines operate at slightly reduced power.
All players would get similar experiences in that area even if they didn't see exactly the same clouds or puddles.