When i was finnished writing i exported the markdown to rtf, 1) selected all the h1's via "select all", set them to be a real (word) h1. vice versa with all other styles i used. 2) Then i put in all the pictures. 3) Then i exported the list from Mendeley.
That process - from markdown to perfection - took me less than 4 hours.
I have some experience with latex and especially latex + komascript, but i hated that experience because the latex sourcecode doesn't ebrace readability and you're sure to get obscure errors in the last second. besides stuff like running latex twice for a table of contents.
Writing
\begin{itemize}
\item really long line which gets wrangled in my vim
terminal, so that i don't see where the second item starts.
\item another long line. maybe 200 characters long?
\end{itemize}
* really long line which gets wrangled as well, but is
better to read because it starts with a clear sign which
is recognized to be a bullet.
* next line, which is also very long.
The older proofreaders could proofread it in the final stage in ms word with the track changes functionality.
I put a lot of thought into Design and Typography and i was sure that i could decide better how my document should look, than latex. I agree, that for some people this is not the case.
After a draft or two, transitions to LaTeX is a must. [Pandoc](http://johnmacfarlane.net/pandoc/) for the win!
Actually the Plan was to typeset it in Indesign, but as i woke up the day of the final layout i just decided to do it in Word.
I'll just pretend it's a parody.
This is what most people do in physics and astronomy. You make the plot in some kind of plotting package and export it to a vector format. In astronomy, the journals only recently started accepting PDF figures in addition to EPS.
In my experience doing all of my figures in LaTeX is significantly more painful than using a real plotting package like matplotlib.
What about tables? Granted they aren't fun to make, but I am not aware of any methods of creating them outside of a latex document.
The point isn't if Markdown has enough features, but rather that LaTeX lets you a pay a price for those features that you shouldn't be paying, just because it's a 40-years-old software.
The best thing about markdown is pandoc.