You could have simple eye-candy effects, as well as gameplay altering effects. For example if there was some acid rain type thing, it could maybe kill any infatry[like some melting effect similar to when they die by radiation] ,sorta like how ion storms instantly killed all airborn aircraft.
Might be a bit imba if it just wipes out all infantry...

Damage effect may be doable though highly annoying. I would like to see global modifications of movement speed or something when it rains or snows as tanks get bogged down.
Other effects could be the whole map going really dark in some eclypse like even, making it pretty well impossible to see. Maybe some buildings would give off light or you could build lights, as this might get kinda annoying as a permanent cycled effect.
Daylight transitions have been done in some mods. As you say, they can get very annoying, particularly in long games. In RA2, many buildings have little lights on for dark levels but if I remember correctly this requires extra shps to make up one building. It can get a bit extreme and laborious.

But you know, different things that could cause different effects, maybe giving benefits or disadvantages to versious units or factions or something. (again, like how ion storms caused the radar to black out, maybe you could have some storm that disables robotic units, would be a real pain for nexus, however there would have to be other balancing effects or such if this was implemented... well, whatever)
To make it faction specific would be imba. You'd end up with NEXUS never being used on such maps. Global effects would be better imo. Exception being the heavy fog that can deny AL spy-sat, which doesn't weaken them all too terribly. Radar blackouts would work but it would be frustrating.
Electric storm that EMPed (like FL electro tower) units near its lightning strikes would be cool, but I am not sure how workable it would be.