Since they’re not really layers in the traditional sense anyway, I’d love it much more if they behaved like tags-- i.e. you could assign multiple tags to an object, which you currently can’t do. That would solve the need for nesting things in complicated groups just to have layer organization.
For example say you have a house modeled with all the furniture. Rather than have a chair group which is on the Chairs layer, inside the Bedroom group on a Bedrooms layer, inside the Floor 2 group on a 2nd Floor layer, you just have the chair group tagged with the Chairs, Bedroom, and 2nd Floor labels.