While this thing was seriously not working, I have actually found out that I’m going to prefer non-Skim annotations now.
Here’s what I’m doing: I’ve an iPad Pro 9.7” with the Apple pencil. I’ve been using it so far a lot with an app called Notability. I also am a long time user of GoodReader. So what I’ve done is to set up my iCloud account on both the side of the Mac as well as the iPad to share data with GoodReader. Then, wenn I’m annotating a PDF using my pencil, on the iPad, I can mostly immediately see those same annotations appear on the Mac, within Skim. Since I prefer handwriting when annotating, it is even more convenient now to read and annotate on the iPad.
The reason I’m using iCloud and not my own Webdav server is that GoodReader is kind of inefficient when synching against Webdav – it tends to re-read the whole file system structure, while on iCloud, it just updates that one file I’m editing. I don’t particularly like iCloud (e.g., on the Mac I had to symlink in the iCloud directory so that I can get to those files without going through the iCloud Finder link). But once set up, it seems to be working… I’ve had duplicates once so far, and may switch away from iCloud at some point – that remains to be seen.
As commented on the Skim forum, I have seen a serious memory leak with the newer PDFKit – the one that came with 10.12.2 Beta (16C32e) – I reported it to Apple. There was no update on my bug report, yet with the relatively quickly incoming 10.12.2 Beta (16C41b), the problem appears to have gone away. Just make sure to observe your swap usage while annotating in Preview, as – should the problem occur again (I’ll update here if I see it) – your system might become quite unresponsive very quickly. But then, that’s what beta versions are for, right 🙂