I'm currently using "PDF Expert" by Readdle. It's a $9.99 app and the annotation features aren't amazing but they're solid and they mostly (see http://forum.paperpile.com/t/metapdf-paperpile-beta-viewer-bug-annotation-text-missing/2939 ) work with the Paperpile Annotation viewer.
The main feature that makes it attractive to me is that I can sync certain folders from Google Drive and have the changes uploaded automatically. In my case I simply sync the paperpile starred folder. However, I have experienced some very odd syncing issues where files would not show up in the app, etc... Not sure what's causing it but it sometimes requires removing and re-adding my google drive account to the app. In general, this is so far the least annoying workflow but it's far from perfect.
The best apps to actually work through documents are probably LiquidText (with inking upgrade), MarginNote or Flexcil (and I guess there are more like these). All of them have cool additional functions that go beyond simulating paper.
However, with these apps (and virtually all other iOS apps) you need to "send a copy" of the pdf to the app. That means that you will later have to export the file back to a pdf (usually losing a lot of the cool additional features) and re-upload that. Because of how Drive seems to deal with files, you can't even just over-write the existing document. I had to go and use the web interface to "upload a new version of this file" if I wanted Paperpile to recognize the pdf as the same document. Maybe the latter issue is something that paperpile could work around on their end, by looking for a file with the same name iff the "proper" file reference is no longer there?
In general I still really like reading and annotating with the iPad Pro & Pencil, but it's currently a bit more hassle than I would have hoped for.
EDIT: I've added "Parallels Access" to the mix for now, especially when I'm working away from the office. With that, I can remote-desktop into my macbook and use paperpile in chrome. It's not good enough for reading papers, but it's good enough for tagging papers as "read"/etc as I read/annotate them.