@gtwilson Regarding dead ebooks, I hear you. I tried keeping notes on the side and it sorted worked but was awkward. Now I'm playing with Notability and rather liking it - finally, I can mark up the pages themselves again! Oddly this makes PDFs better than ePubs and such for my use now.
I never understood why the Kindle's support for displaying my own annotations was so anemic. Don't bury my remarks behind a footnote link - set them like asides right there in the text where I can see them!