I know you are planning realistic 3d clouds, but I would just like to post a reminder at how significant accurate atmosphere simulation improves the feel of the simulation.
Here's an example of a unity engine atmosphere renderer that looks really nice (you can try a demo too). Rain, fog, and mist are especially interesting.
Here's to hoping you have time, patience and energy to get a better atmospheric renderer in soon!
Wait guys! I plan to have realistic animated 3D clouds with global illumination and light scattering, self shadowing, god rays, rain and snow, lightning and thunder, cyclones and tornados... But it is a lot of work. Currently I work on spaceships, physics, navigation, GUI, and procedural galaxies simultaneously, but adding clouds now will delay version 0.96 release till 2013... Because clouds requires rewriting of the engine to a deferred pipeline, adding shadow mapping and adapting the landscape system for animated surfaces, etc.