I wrote mine in Latex, along a team mate witting in Word. Her onboard was way faster, but she had to fight really hard in the end for Word not messing up everything on the smallest changes.

Meanwhile, when I had a decent setup I could move a whole section from the intro to the results and the overall layout didn't suffer (floating tables, figures and code still in place, references still pointing where they should). I had code snippets with colour highlights imported from the actual source code (good luck trying that in Word). I could insert the companion papers with a single line of code per document, and they looked great. I even had a compilation flag to output the ereader version.

My take was that Word enabled my team mate to kick a lot of cans down the road (but the cans eventually came back), while for me the reverse was true: build a decent foundation, and after that it was all pure write-cite-compile.