There are some good discussions online about the relative merits of different types of software for writing long scholarly documents like a PhD thesis. For instance, Amrys O. Williams’ “Why you should LaTeX your dissertation; or, why you don’t have to write your dissertation in Word“.
I’ve seen the plusses and minuses of using LaTeX in academic and activism contexts first-hand and the dominant set of considerations for me concern collaboration. Theoretically, as a free and open source typesetting system LaTeX ought to be ideal for preparing complex documents. Unfortunately, whether they are university professors or student activists, it’s likely that few or none of your potential collaborators will already be familiar with LaTeX syntax or comfortable providing comments on a document in the format of LaTeX source code.
For my dissertation I have decided to write the whole thing as chapters comprised of Microsoft Word files, for the ease of my committee members. They won’t have full citations, but just the unique identifiers and any other details which I will eventually need to produce a citation in LaTeX. This way, my committee members can provide comments on Word documents and, once I have everything nailed down, I can spend a few days moving all the text into LaTeX for the preparation of the final dissertation. This way committee members also won’t be distracted by a need to minutely copy edit formatting and other trivialities, since each chapter explains that it’s just a draft for review with precise formatting to be done later.
I would rather just write the whole thing as LaTeX code in TextMate, avoiding the need to use Word at all, but a central necessity of writing a doctoral thesis is soliciting and incorporating input from committee members so all told the approach of writing in Word and later typesetting in LaTeX seems to have the most to recommend it.
Continuing to work with my Word dissertation draft, I am annoyed every day by the program’s weirdly broken search functionality. Once it finds a search string in a footnote it will then only show you other places where it shows up in footnotes, not in the body text. At the end of the document, it then annoyingly closes the document map sidebar and opens a useless footnote window.