After thinking about the pros/cons of Scene Assemblies and because of the fact that we have switched to Arnold for this project and then I presume that we are not going to use that much render layers anymore, we've decided to give Scene Assemblies a shot in one of our complex sequences where we really need to render everything as ASS files.
The only thing that we are avoiding was doing per face shader assignments, but we were happy with being able to assign shaders to our referenced assets in lighting scenes.
I think with Scene Assemblies, if we need to have a custom shader setup on the assets then we should do it on the Assembly Definition and this way it is going to make things cleaner and consistent. Also, there are AOVs that we still can use to render custom passes etc.
Also, I had this very old shader assigment system of mine. I was using it when Maya was f*cking the shader assignments on referenced assets a lot, then I've written this custom system which was restoring the shaders at render time (with pre-render layer mel scripts). I may develop it further to handle shader assignments on Scene Assemblies, don't know.