I've captured (in Evernote, ironically) a few Evernote alternatives. Haven't had time to look them over yet, so not sure how much they address each of your needs:

- https://getpolarized.io/: open source html and pdf document manager. Supports Anki flashcards, local storage, markup of pdfs, tracking reading progress, more

- https://www.notion.so - paid/hosted service

- https://joplin.cozic.net/ - seems like a decent open source project

If you check these out and respond here (or in a new "Tell HN") with your thoughts, I'd love to read it.