Markdown is very limited and you will soon hit a wall, when you get down to writing a thesis rather than a paper. For example if you want to write something to

Markdown is very limited and you will soon hit a wall, when you get down to writing a thesis rather than a paper. For example if you want to write something to the Table of Contents which is not the section title itself. \section[short]{Long Title} It is also possible within pdfLaTeX or LuaLaTeX to write shorter commands. A GUI will eventually slow you down and is impossible to cater for the hundreds of commands including commonly used packages.