great plugin idea!
Does your plugin add a link to post pages, i.e.
<link rel="alternate" type="application/epub+zip" title="EPUB" ref="..." />
I imagine this can be very useful for tools that grab/convert EPUB from websites; they could look for such links first before attempting to create something themselves.
Do you already create EPUB 3? If not, when do you intend to switch? In particular, I have posts that contain math; EPUB 2 does not work too well with that.
Can you add an option to turn off explicit EPUB storage? I don't think they would be requested too often so I would like to avoid persistency of snapshots of dynamic data. If you want performance, caching plugins should do the work. Is the plugin built such so they can?