Earlier quoted context omitted.
Writing a thesis using only markdown sounds extremely painful. Are you going to create all your figures elsewhere and then include them as images? How are you going to create your list of figures? And your table of contents? How are you going to create, maintain, and organize your list of references? I could go on.
> Are you going to create all your figures elsewhere and then include them as images? 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 plotti…
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.