It would be nice to have a checkbox to show/hide clouds in the staged mission editor. Sometimes you need to have "View Terrain" checked so you can plan taxi, landing/take-off patterns, or other terrain specific planning.
If you have a weather file defined, it loads it automatically by default. The clouds bock your view of the terrain if you are zoomed out to a useful distance. Loading the clouds is probably seldom useful in mission planning, but just in case, have a checkbox to turn it on or off.
Similar to how the terrain editor lets you check trees on and off.