Sounds like a great idea! I loved those old cloud banks in Aces High 1 and was sad when they got replaced by the 2d clouds of AH2... I remember ducking in and out of clouds to lose zeros in my P-40 back in the CT, which's impossible with the 2d cloud textures.
The maps are so big that I think you could have localized bad weather roll through and only affect a base or two at a time... nothing game-breaking.
...imagine the whines (and log offs) when the entire arena is disrupted.
That sounds more like the old 'Night' ...everybody really did log off then. Weather doesn't have to be an arena-wide thing.