iAnnotate (US$9.99) is a full-featured iPad app for marking up PDF files with highlighting, diagrams, notes, and even audio comments.
Standout features include the ability to markup DOC and PPT files as well as PDF documents. The app allows you to have eight documents open at once, something many of its competitors don't offer.
There is a broad arrange of annotation tools, and you can create custom toolbars to speed your work along. For importing you can use Box, Dropbox, Google Drive, Microsoft OneDrive or WebDav, plus iTunes file sharing is supported. The app doesn't support iCloud, which is a negative, but Air Drop is supported. You can also open emailed PDFs.
Documents can be searched quickly, and you can create folders to keep projects in a workable environment.