I finally found it: the best workflow for reading PDFs for research between my MacBook and iPads.
I mention this as an announcement because I've been at this for some time. I often need to read a lot of PDFs for something or other, and I hate to print them all out, but it gets dicey to annotate them electronically. The annotations get lost or sync oddly, and occasionally the entire PDF disappears.
In the best of all possible worlds, I could drag my research into Scrivener, and it would all sync somewhere, and I could mark it up somehow and have it sync back to Scrivener. But that in no way works. No part of it works. I don't even use Scrivener for keeping my research.
I used to use Evernote, and I've tried Pocket and NoteSuite. Evernote now has the ability to mark things up with Skitch, but it's cumbersome and makes copies of what you've marked up. I don't need to spend hours managing my research materials. Might as well print it and drag it around at that point. NoteSuite has promise, but it's still a bit crashy. It's new, so I've got my eye on it.
At the finish I've been solidly using Dropbox and PDFPen. You can set PDFPen on the iPad to sync Dropbox folders, so if you download a PDF to an iPad and annotate it, the changes appear on your Mac. For some reason I just figured this out; I thought PDFPen required iCloud, and that introduced the multiple-copy problem yet again. But the Dropbox solution is perfect.
I have my Scrivener file, and I have my own little systems there for keeping track of research (none of which involve storing the PDFs in the Scrivener file). Then I have a folder in my Dropbox "Action" folder for each project I'm working on. My "Action" folder is synced with PDF Pen.
It's the little things in life.