I don't like embedding either, but I think it's here to stay. For whatever reason, many people appear to be more prone to adopt an addon if they don't have to download a separate addon to make it work.Just a (perhaps) crazy idea. Forget about embedding completely. Chuck all libraries into a zip-file and ask users to download and install that.
I agree that changing the zip script seems to be the way to go. That way, it could be setup to simply not include any of the embeds or the embed.xml file.
How would this affect authors who didn't update? It would still be pretty much the way it is now, wouldn't it?