It would be amazing to be able to view and annotate locally stored ebooks (epub, mobi, azw) and PDFs within Memex. Existing readers are very limited in their capabilities, especially for the search/export/use of annotations - I think a big part of the problem is that epub files don’t intrinsically support annotations, so each tool builds their own proprietary system. Additionally, it would be great to be able to combine notes from books with related articles within a single tool and collection.
It looks like Hypothesis has an integration with a couple of open-source ebook viewers - epub.js and ReadiumJS. https://web.hypothes.is/blog/epub-annotation/. I hope that you could do a similar integration someday!