I have been using Rex Sky Force since it was released, and it is an amazing program. It does "model" clouds (I don't know how they're modelled either, but they are) and produces a number of new models to give a much greater variety of cloud models. It just produces some amazing looking weather. It has many more features apart from just clouds too.
I have also been using the Sky Force weather engine exclusively in P3DV4, mainly just to test it out over a long period. That was a bit clunky, but still replicated real world weather very well. The only complaints I really had was that simconnect was used so when an update was injected in to the sim there was a slight pause, but worse than that the sky would suddenly change from thick overcast clouds to zero clouds in an instant. Also for some reason the baro pressure reported by Sky Force was never the same as that experienced in the sim. A massive update has just been released this week, so I'm hoping these issues have been fixed or improved.
Another thing it can do is generate sky textures that change over (I think) a ten day period, so you choose a set rather than a single theme. So each day you fly the sky will be changing. Same as with the weather generation. By using the various cloud models and textures the changing weather will dynamically be replicated in the sim as you fly.
There are too many features for me to continue with, so just check out a feature list (and an update list showing the new fixes). I can honestly recommend this program to anyone.
Cheers,