i used to like PDF expert because i could drop pdfs into it using a browser or iTunes drop into folder on the iPad. I purchased the app and used it fine for a long time. when i emptied my iPad for sale, I managed to get all the PDFs off.
when i went to get it for my other devices it asked to charge me again for the new version. some of the features are pretty good, some I couldn't get to work right, like listing pages for reference which is easy to do but at the time I couldn't get them to print. that may have changed.
having isolated apps leads to PDF copy duplication if that annoys you at all.
i haven't gotten the new version since I no longer use the iPad.