I have been testing Margin Note to mark up assignments from university students. I see one major and a few minor issues.
Margin Note flattens all of the annotations for exporting. Granted, it makes up for this failing by allowing the annotations to be exported in a separate OmniOutliner or mind map format. But, when one’s only goal is to markup and then review in a different app (e.g. DevonThink To Go), the loss of annotations is a failure. Also, Margin Note at least handles importing of annotations from PDFExpert properly.
The sync with iCloud is inconsistent and at times unreliable.
Importing only works at the root level, not in sub-folders.
The lack of support for Google Drive and Dropbox and other cloud services is a limitation.
The fixed toolbar position at the top is restrictive (compared for example to PDFExpert with options for any side of the screen).
Overall, I am pleased with the options that Margin Note provides. I especially like the options to tag notes. This allows me to use metrics such as #incorrect, #invalid, #sloppy, #improper, and others. I can then tally up the scores just by counting up and scoring the tags.