We do already allow for some random weather factors in Scenario design (specifically Hurricanes/Tornados/Typhoons & Earthquakes), so those may make it in given time.
Seasonal flux in crop production would also be very cool to have, though I'm sure it will confuse some players (ie, "hey, why is my production down so much this past month?") We may make it game option then.
Though rain, mud, and snow would be cool additions - what would a march on Moscow be without the mud of autumn and frozen snow of winter? Just ask Napoleon and Guderian about the effect of weather on a good battle plan
Weather effecting unit movement, resupply, morale, etc would all be nice touches. So would freezing rivers and lakes. It's still on the feature list, but it has to pull in its toes from the chopping block every now and again...
PS - yes, I know that technically an Earthquake is not a "weather event"