You might not like it but many ebook readers have annotation support. Usually you can highlight text and add notes. In the case of Kindle, you can later find all your highlights and notes on:

  https://kindle.amazon.com/your_highlights

There are browser add-ons that make this page better and easier to export. One example is http://www.norbauer.com/bookcision/ which will allow you to download your notes in XML, JSON or plain text.

Personally, I don't use the online notes page. I am more than happy with the device showing me my own notes. There are also options for showing popular notes and highlights.

I agree that it is not frictionless like pen and paper, which I also love, but for those like me that live in far away countries where up to date books are expensive and hard to find, being able to use ebooks from abroad and use the notes features is a blessing.