PDF is a terrible format, but it is the standard in academic, despite some perfunctory efforts to make like the rest of the world and get with ebook formats. That would be nice; but in the real world, ebook formats are the minority, and generally if you convert PDFs to ebooks the equations turn into poo, so this is only a liberal arts solution.
Now, how will you read all those PDFs and annotate on them without losing track and going crazy or losing your annotations? Bonus points if you can sync your annotations to your citation management software.
- Zotero can sync annotations and store PDFs with metadata conveniently. See citation management for the details.
Calibre - mention
Built-in reader does not support PDF annotations.
Sync to the device using a sync service of some kind, then read the PDFs using Acrobat, or Foxit. Maybe try xodo?