Yes saving layers-per-page is definitely on the wishlist, as is saving
Graphic/Annotation Groups per page
(http://code.google.com/p/arcmapbook/issues/detail?id=9). You could
achieve the specific use case you mention with mapbook now by setting
Visible Scale Range[0] for each of the layers in combination with the
mapbook variable scale per page option.
[0] Displaying layers at certain scales -
http://webhelp.esri.com/arcgisdesktop/9.3/index.cfm?id=220&pid=211&topicname=Displaying_layers_at_certain_scales
cheers,
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-matt