Adam Engst, writing for TidBITS:
It pains me to say this, speaking as the co-author of “Take Control of Preview”, but I have to recommend that Sierra users avoid using Preview to edit PDF documents until Apple fixes these bugs. If editing a PDF in Preview in unavoidable, be sure to work only on a copy of the file and retain the original in case editing introduces corruption of any sort. Smile’s PDFpen is the obvious alternative for PDF manipulation of all sorts (and for documentation, we have “Take Control of PDFpen 8” too), although Adobe’s Acrobat DC is also an option, albeit an expensive one.
What went wrong? Engst quotes developer Christian Grunenberg:
Apple wants to use a common foundation for both iOS and macOS. However, it was released way too early, and for the first time (at least in my experience) Apple deprecated several features without caring about compatibility. And to make things worse, lots of former features are now broken or not implemented at all, meaning that we had to add lots of workarounds or implement stuff on our own. And there’s still work left to be done.
In other words, parity with iOS took priority.
On the bright side, when this happened with the iWork suite, the Mac apps eventually gained back most of the functionality that was removed for parity with iOS. But it sure seems like Apple pulled the trigger on this at least a year before it was ready.