I use GoodReader constantly - every day, near enough. Reading journal articles is a big part of my life, and GoodReaderProPDFEditor lets me organise them logically, highlight and annotate, view my annotations easily, copy-paste text, and flip from one article to another really easily.
It's also possible to do a split-screen, with GoodReader on one side and a notebook app on the other, which is the most efficient and intuitive way I've ever found to take notes while reading.
Setting up sync (with Google Drive, in my case) can be a bit trial-and-error at times, but it was well worth it - I know I won't lose my annotations and my archive of articles I've read, whatever happens.
GoodReader is one of the few apps I genuinely would be distraught to lose!