I think we can agree a continuous weather model really benefits this kind of clouds.
(Trying to keep terminology clear: Please do not refer to this as a 'weather model' - it's just a way to render a cloud layer, clouds are only a small part of weather modeling).
For stratiform clouds, sub-dividing them into single 'blobs' as we currently do is definitely not particularly good - in fact, for those a meta-description 'draw me something roughly in that area' would work perfectly fine.
We had some nice complicated high undulatus patterns here yesterday which are probably on the other end of the scale - I (sort of) have a function to generate them, but it's complicated and I'd want this offline, noise really can't do this fast enough and they divide into single blobs naturally.
So generally I was thinking a descriptive texture by layer. The texture gives us four channels - so we use red to bias the noise function to 'force' clouds in certain spots, green to encode the difference in altitude to the layer altitude, which gives us two more channel to encode shape and density parameters.
If we want to generate a layer, we just color the red channel uniformly, if we want to have single clouds we write into certain spots only. The smallest clouds we need to define solidly are perhaps 50 m, so a 4096x4096 texture sheet could give us a 200x200 km area covered.
So rather than place a quad in the scene, the cloud generating function would simply write a red spot into the texture.
(Of course the texture somehow needs to move with the airplane, or a set of tiles of such textures needs to be instanced and deleted,... but I believe that can be made to work).