Bulk re-naming of layers
Allow users to select multiple layers and re-name them all at once. I prep layered files all the time for use in AE and often have layers that are all the same type (eg: box).
The user could shift-select the layers, then right-click and select "Re-name layers". Perhaps there could be an extra option (checkbox) to automatically number them, based on the order in which they were selected.
Alternately, you could add a keyboard modifier - so if they re-name a layer by double-clicking it, then if they hit Shift-Return, it would activate the name of the next layer down in the stack (Option-Return would be for the previous layer).
Mike, for now use this awesome free script by Sergey Osokin to do that: