For PDFs, I use Documents by Readdle on iPad. Great for the markup and includes syncing (files accessible offline). Lots of options for the latter (OneDrive, Dr

For PDFs, I use Documents by Readdle on iPad. Great for the markup and includes syncing (files accessible offline). Lots of options for the latter (OneDrive, Dropbox, iCloud, I use WebDAV), although syncing is a pain because you have to keep the app open (it seems to be an iOS limitation). For EPUBs, sadly, it doesn’t do highlight... for this I think you could use Marvin, which can read from a Calibre Server.