Many people prefer to read papers printed out, pen in hand. In the web app at app.axsuro.com/pdfs you upload a PDF, up to 50 MB and 200 pages. Axsuro gives it back to print, with room to write and a code on every sheet.
You write your comments on the sheets, photograph them like any page and get the original PDF back, with your notes as comments where you wrote them. Markers such as todo: work there as on any page.
Axsuro is not a reference manager. Keep citations, references and bibliographies in the tool you already use.