Documents by Readdle is a useful file manager, image viewer, cloud synchronizer, pdf reader and download manager. PDF-Reading has however only limited annotation support (notes in text and highlighting), while the ≈10€ Readdle PDF Expert should extend these abilities.
However, I am slightly reluctant to purchase PDF Expert just yet, because I couldn't find out if the App integrates well with Documents; Since iOS usually doesn't give apps direct access to each other I fear, that syncing annotations made in PDF Expert back to Dropbox would require synching my pdfs to both apps -- aside from the obvious waste of space, this also brings the risk of file version conflicts.
Documents can send a PDF to Adobe Reader for annotating (quite powerful too), but it is then saved as a copy local to Adobe Reader with no way to move it back to Readdle directly. Worse yet, after doing so I have to versions of the same file; Such file duplications are one of the most annoying issues I have found with managing data on mobile devices; iOS just makes it especially common due to the (otherwise justified) high level of app-isolation.
I fear that the same would apply to PDF Expert though PDF Expert should at least be able to use DropBox.