@mz2 Thanks for your comments.
This is the third time I've tried using this reply system. The first two tries caused Firefox to lock up.
but our focus is a little bit different to that of LyX in that the mental model it gives one is very much centred around that of LaTeX (please do correct me if I am wrong)… whereas Manuscripts is more generally a structured word processor which cares deeply about the semantics and separation of presentation and content, but treats LaTeX certainly at 1.0 as an import and export format to an editing experience that is close to WYSIWYG (in both cases of LyX and Manuscripts the model is more What You See Is What You Get Where It Makes Sense).
I would describe LyX pretty much as you describe Manuscripts—separating content from presentation while providing with clues to the writer as to what is going on e.g. different size and bold text for section names, centered title, rendered math, etc. The reason I use LyX is that i don't want to write code (LaTeX) while writing papers, and LyX lets me do that—I never have to think about LaTeX ever. In fact, I don't know LaTeX, and that is the whole point, except...
I recently submitted a paper for which the publisher wanted two versions; article class double spaced with wide margins and ieeetrans which is single spaced and two columns to estimate how long the paper would be. In LyX, I just switched document class and that's it, except in the double spaced version looked odd, double spacing the title and author info. It was super easy to leave the LyX setting for single spacing then insert the command for double spacing right after the author info.
So that is why I asked about inserting arbitrary LaTeX; it can be really handy and even LyX doesn't handle all possible LaTeX code. (The LyX community calls LaTeX code Evil Red Text because it is rendered on-screen in red type.)
LyX uses its own file format and only generates LaTeX when you tell it to do that. Typically you would use LyX like any other (structured—your nice word) word processor and only think about exporting to LaTeX when and if the publisher requests it.
When writing in LyX and you want to see what your work looks like, you just hit Command-R and in a few seconds or less it is rendered as a PDF and opened in a PDF viewer such as Skim—that's it—no fuss. You can jump from a place in LyX and Skim scrolls to the same place and puts a red dot on screen for a couple seconds; the reverse, Skim to LyX, works pretty much the same way.
You can export from LyX to several file formats: LaTeX, Word doc and docx, odt, PDF, Postscript, HTML, XHTML, plain text, RTF. Those are the ones that are currently active on my system; I think you can get others. Some exports are more complete than others but LaTeX is the best, and that is why some people think of LyX as a friendly front end to LaTeX even though it is more than that.
Control-clicking on a figure or table or other external material can cause the object to be opened in its native editor. Changing figures on disk causes them to be automatically updated in LyX.
In my original post I mentioned the excellent palette-based/command-based method of quickly and easily entering text. It has easily-learned modes that make this very efficient. For example, to enter beta, one could use the mouse/palette, one could type Control-G (for Greek mode) then b, or one could type \beta. Something like that would be really great in Manuscripts because as I understand it, as of now you have to actually enter LaTeX for your math etc.
Sorry for the rambling. I'll be checking out Manuscripts as soon as I upgrade past Mavericks—long story.