Writing my thesis with markdown was one of the best decisions i made. I wrote 99% of my master thesis in markdown (50 pages w/o interviews). 1) I didn't have a lot of images so i just wrote FIXME: Image Foo.png where they belonged. 2) I wrote my Citations Plain in there (e.g. Wocken, 1985, 7 ff.), using a special folder for all sources i really used in Mendeley. 3) Writing in markdown i could just c&p perfectly formatted chapters written with simplenote. 4) i also could seperate the chapters in files and keep everything in a git repo.

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}

is complicated and you can't read it well. this otoh is very easy to read:

  * 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.

Easy readability is crucial, because i needed proof readers. The young proof readers could actually get the markdown code and correct my mistakes there (or write comments, starting with another fixme). really rocked with diff.

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.