i used word for a large project (undergrad project report of 100+ pages with 4 member team) in 1997 and even then word had features for most (if not all) of the items in your list:
* large docs can be handled by splitting them into master-child documents. You can format across all child documents from the master.
* figures can be edited in-place or embedded from original source.
* collaboration was possible then with child and shared docs, it should only be better now.
* citations and refs are supported, although I dont know if all styles of citations are.
* templates have been in word from a long time and imo are quite natural because they're prototype-based (ie, you can make any document AFTER you create it into a template. other documents that use that as a template inherit all styles and so forth)
* the visual "View changes"mode in word is quite natural and even allows for some offline discourse with your collaborators as each user's comments and changes are marked with a different color and comments are allowed.
*words symbol editor (which also existed pre-1997) is quite up to the task of most equations (again, imo; i've not done a lot of hairy equations)
word is just a better tool for large documents, and i say this asn ardent anti-ide guy. my preferred setup for code documentation is sublime text and markdown; but when you want to Just write a document, word it is.