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.
It sounds like you want something that you can customize for your particular wishes. Have you considered taking matters into your own hands and using the programmable Emacs?
I have fiddled with emacs some over the years — really wanting to use org-mode more than anything else — but I just don't have the time to pursue it. It would take me quite a while to enable it to do what I need, if I could ever manage it, so I've waved goodbye to emacs.
Well, to each his own. I've never read the 438 manual, and I don't plan to. The video tutorials got me started. I don't use all of Scriveners features—I don't think anyone does—but they're there if you need or want them. I'm puzzled because it seems easy to ignore a feature if you don't like it. I like that I can keep just about everything in a writing project well organized and one click away in one file. When I want to get serious about writing, I just flip into full composition mode, and everything falls away leaving just my writing. Scrivener will be perfect when the iPad version comes out.
I don't use Evernote either. It's an amazing program, but I prefer to do my organizing within Scrivener. I also use FileMaker.
Anyway, good luck in your search for a program that fits your needs.