Here are some operative burning questions:
1) Will cloud-obscured icons be a simple 'see em or don't' or will they be subject to partial masking like the plane object itself? My vote is that icons are yes/no, and the actual plane, or dot might wink in and out...
2) Will we get all kinds of cloud formations? For me, it's not enough just to have them in one alt band, or in one form. Do it right, and have times of low clouds layers (pissing off our high alt laser-Norden buff guys), have some wispy, thin strata other times, have big puffy thunderheads other times, etc.
3) Hiding in clouds: everything I've read suggested that air in many clouds was so violent and unstable that people did NOT make a habit of staying in clouds for tactical benefit. Perhaps momentarily, and of course as an escape maneuver, but not as a stalking method. They would use the cloud to keep between them and an enemy for time, is my understanding. Will the violent air also be modelled in the clouds that had them?