I have noticed that when something is saved via 'Save selected', all the empty layers in the scene get saved too. That can lead to lots of tedious clean up. Could it just save the layers that the selected objects are in / use ?
That leads me to the layer management suggestion, which is could deleting empty layers either also delete any nested ( empty ) layers, or give an additional option to delete nested layers ? This not being the case can also lead to a lot more clean up of a scene than should be necessary ( I think ).
Thanks !