I'm still sour about the 3 days it took me to have something usable for my thesis, and I was starting from an existing template. And it's still not exactly how I want it to be; I gave up on addressing a bug in the reference list.
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.
Another ergonomic benefit is scripting. For example, if I'm running a series of scripts to generate figures/plots, LaTeX will pick up on the new files (if the filename is unmodified) and update those figures after recompiling. This is preferable to scrolling through a large document in MS Word and attempting to update each figure individually.
As the size and figure count of your document increases, the ergonomics in MS Word degrade. The initial setup effort in LaTeX becomes minimal as this cost is "amortized" over the document.