Strangely enough though for the current paper I have to write (> 20,000 but < 40,000 words) I have decided to see how far I can get with Markdown, Pandoc, and a lightweight custom pipeline. I'm going on a hunch but I have the feeling that this will work out ok. I may be wrong. Pandoc will auto-gen a table of contents from the Markdown headers. I'm going to try and grab citations straight from Zotero. AnnotateJS will give me endnotes but also allow others to make annotations and I should be able to generate HTML5+RDFa for semantic annotation. And yes, PDF because the university requires it -- I think I'll be able to go to PDF via LaTeX with Pandoc. Markdown does blockquotes too. I don't need complex Math, but I will need notation for propositional/predicate calculus. There really aren't that many _elements_ in an academic paper when you break it down to its constituent components and Markdown+extensions seems to have it all covered.
Pollen, which featured here recently, looks interesting too and I'm going to investigate that.
Edit: I've used Overleaf (and love it!) and even demo'd it to others and I think it's a great product. Scrivener is doing interesting things as well.