One thing I like about PDF is the annotations (notes & highlights) are embedded in the PDF itself. That is not the case for EPUB files, each EPUB reader stores annotations in its own proprietary format.
Very true, I just rolled out annotations for Kavita (a self-hosted book/comic server) and epub doesn't have the ability to store it in the file (although Kavita has a no-modification policy).
Although for cases like Kavita, storing in the file would be problematic if multiple users want their own annotations without concerns of data leaking.
Although for cases like Kavita, storing in the file would be problematic if multiple users want their own annotations without concerns of data leaking.