I was also unhappy with how reference managers handle annotations. So I rolled my own app (https://getcahier.com), with highlight management integrated in the application. This enables me to extract highlights according to topics, organize them in notes using document elements (like collapsible notes and outlines) and use them to plan more complex arguments. This makes it much easier to read actively.
On the paper organization side, I would also like to find out a better way of doing it. What helps me a lot, from a more methodological perspective, is to categorize books according to time period, school of thoughts, or perspective.
On the paper organization side, I would also like to find out a better way of doing it. What helps me a lot, from a more methodological perspective, is to categorize books according to time period, school of thoughts, or perspective.