I wrote my MA thesis using markdown (with extended syntax). Structuring the document is easy: just use one hash for top level sections and more for subsections. Footnotes are easy, you just add a footnote[^reference] somwhere and then add the footnote text on a seperate line somewhere:
[^reference]: some text
Inline math works by adding $x= \frac{y}{z}$ or in a seperate math block by adding two $ signs before and after.
The syntax of markdown is easier there, but LaTeX is arguably much more powerful, e.g. you can load tables from csv data, generate graphs, make it deal with your bibliography, draw circuit diagrams etc. And the layouts tend to look just good.
I ended up converting markdown to Indesign IDML and using this as a source in an Adobe Indesign layout where I could do all the basic typographic settings and styling once and update it on changes.
The syntax of markdown is easier there, but LaTeX is arguably much more powerful, e.g. you can load tables from csv data, generate graphs, make it deal with your bibliography, draw circuit diagrams etc. And the layouts tend to look just good.
I ended up converting markdown to Indesign IDML and using this as a source in an Adobe Indesign layout where I could do all the basic typographic settings and styling once and update it on changes.