The standard include/exclude can work well in most cases but falls short when you have objects in XRef Scenes.
I would love it if I could include/exclude objects by layer for material override/lights/caustics/masks/render selection etc.
Example 1:
"Artist A" is working on the lighting of a scene and wants to see the cladding of a tower block that is in an XRef, whilst "Artist B" is still working on the model in the XRef.
Artist A either has to work without being able to see the material, or merge the XRef into the scene and manually update once "Artist B" has finished - losing one of the advantages of XRefs
Example 2:
A landscape file including plants is being shared by multiple artists and looks great in most renders, however in one scene some lights are affecting the foliage in a way that doesn't look great
The artist working on this shot wants to exclude those plants so that the rest of their shot can stay the same but remove the lights from the plant and knows that they are on a specific layer.
Once again they would have to merge the XRef into the scene in order to achieve this.