I use zotero and store the pdf files (renamed and organized with ZotFile) on OneDrive. I can read papers and make highlights/notes to pdfs and they will sync to all of my devices. These notes can be extracted and made searchable within Zotero by Zotfile.

At first I preferred the way that Mendeley did this with its built in pdf reader, but now I'm happy Zotero delegates to the pdf software of your choice.

If you were on the iPhone mac side, papers had a brilliant solution that was appealing