AFAIK, nobody has added the weather to Stellarium, but it does show sky at various times and places on Earth, with toggles for the ground and atmosphere. Web version:
After all of that, I have to ask why would one want this anyways? If it's cloudy outside so I can't see the sky, I don't want a tool to show me the same no sky view either.
How do you expect to get global realtime cloud coverage?
You can also pull from Doppler radar sites (real time, limited to ~ 250km radius about sites), mosaic and interpolate with MODIS