The bigger your writing project, the less likely it is that you’ll find a writing environment that’s adequate to your needs. When you’re writing a book, you need to find some way to juggle research, ideas, notes, drafts, outlines … which is hard to do.
As far as I know — I’d be happy to be corrected — the only product on the market that even tries to do all this in a single app is Scrivener, which many writers I know absolutely swear by. Me? I hate it. I freely acknowledge the irrationality of this hatred, but so it goes. I can objectively approve of the quality of an app and yet be frustrated by using it. I have the same visceral dislike of Evernote, though in that case sheer ugliness is the chief problem. But both Scrivener and Evernote are created by people who follow the more-features-the-better philosophy, and that’s one I am congenitally uncomfortable with. (The user manual for Scrivener is over 500 pages long.)
A few years ago I thought my answer for big projects might be Ulysses 2. I couldn’t put PDFs in it, but I didn’t mind that because I like to annotate PDFs and you need a separate app to do that properly; and in other respects it had a lot going for it. I could write in plain text with Markdown, and could always have visible onscreen notes, or an outline, for the chapter I was working on and even, in a small pane on the left, the text of another chapter. Also, a Ulysses document was basically a package containing text and RTF files with some metadata — easy to unpack and open in other apps if necessary.
I liked Ulysses, but it tended to be unstable and some of its behavior was inconsistent (especially in exporting documents for printing or sending to others). I was pleased to learn that the makers were working on a updated version — but surprised when Ulysses III came out and proved to be a completely new application. And after I tried it out, surprise gave way to disappointment: essentially, it seems to me, it’s now an ordinary document-based text editor — an attractive one, to be sure, but not at all suited to the creation and management of major projects. As far as I can tell, you can replicate all the features of Ulysses III, except for its appearance, for free with TextWrangler and pandoc.
I use phrases like “it seems to me” and “as far as I can tell” because Ulysses III is getting some good press: see here and here and here and here. But these tend to focus on how the app looks, how well it syncs with iCloud, and its export options — not its status as an environment for organizing your writing, especially a project of any size. Ulysses III seems to me a nice app if you’re writing blog posts, but if you’re working on something big, it’s a significant step backwards from previous versions of the app.