In this old but apparently still popular paper, Allin Cottrell Allin Cottrell argues that a word processor is a "stupid and grossly inefficient tool for preparing text for communication with others." The main argument is that "preparing printable text using a word processor effectively forces you to conflate two tasks that are conceptually distinct and that, to ensure that people's time is used most effectively and that the final communication is most effective, ought also to be kept practically distinct." In other words, WYSIWYG is "evil."
Instead, the author argues that we should all use TeX and that it would be best to use it with Emacs. If you use Unix or Linux, this approach might end up looking roughly this way:
I am not sure this is the way to go. TeX is not for the faint-of heart. Indeed, the conceptual overhead of TeX, or perhaps better: the amount of time you will have to invest in learning and maintaining the skill you need, will for most people rival the amount of time spent in uselessly formatting documents in a common word processor. Of course, if you have to work with complicated mathematical or logical formulae, you might hav to use it. But for most of us, it would be overkill.
It seems to me that a better way to go is to use a light-weight lightweight markup language, like Markdown or ReStructuredText. Scrivener, for instance, uses a version of Markdown called MultiMarkdown. Another approach would be to some kind of Wiki Markup—which, of course, is precisely what I do.
This is a middle way between using a fancy word processor, like Microsof Word, and Amish Computing or Lo-Fi writing.
In the end, however, you will end up submitting your work in "rtf" or "doc" format anyway. You don't have to use MsWord, however. I use Atlantis which allows you to save your files in a variety of formats, icluding rtf, doc, and even docx and OpenDocument (ODF) format. It does both footnotes and endnotes in the same document, something which MsWord has never been able to do.
What is really needed, I think, is the capability of easily transforming documents written in some kind of markup language to rtf or other word processing formats. Scrivener has these features, and that makes it most interesting in my view, not the fancy-schmantzy index card metaphor and the lame outliner.