I looked at Skim to see if it was a useable and easy PDF reader and note-taker for my laptop.
I thought it would be a good app for reading and annotating long texts, or even short texts with lots of annotations in a small space that may get lost amongst each other.
The really good thing about Skim is there are two sidebars - one which shows pages of the file, and another that shows every edit, note, highlight, strikethrough, etc. on the file in page order.
You can hover over chapters in the content sidebar to view a thumbnail of their contents. There’s also an optional reading bar to help you focus on the text.
You can keep any of the notes on top, to be easily compared. You can take a snapshot of a section of the PDF and store it in the notes sidebar to refer back to easily. You can also tag notes.
Skim has extensive support for scripting and a number of AppleScripts available.
The ‘notes as text’ functionality exports: highlighted text, underlined text, boxes, anchored notes, and circled passages in the .pdf text, along with the page number the note was made on. The result is the same whether the exported notes are saved as rtfd or .txt. Notes can also be saved to a separate .skim file or indexed by Spotlight.
One downside is that notes cannot be exported as a .pdf and read in Preview, nor in iBooks. As a PDF bundle it works, but only opens in Skim.
Although notes cannot be automatically converted to Markdown, but there is a script to export notes from Skim into Markdown, which could then be read alongside a copy of the PDF. Another script formats notes into markdown and embeds hyperlinks back to the individual pages of the source PDF.
After using it to read three different texts (two long ones, and one article a few pages long), I would say that I would probably use it for big readings, but not for more casual text or articles.