good to hear that you are targeting bibliography tools (i was going to ask about that). I hope you have a developer who is familiar with strength of the Latex+bibtex+hyperref ways of working.
In my group no one would even consider writing a thesis in anything but latex. I dont think there is any inherent reason that a word processor could not compete.
Another related issue is internal referencing. So i can give a label to a figure or table, reference the label, and automatically get Figure 23 (where the 23 if automatically updated) which will be hyperlinked in the PDF to the figure.
To get scientist you will also need similar strength in equation formatting.