Here is what I think about writing in Mathematica. For quite a long time I thought that Mathematica can be used for nothing else but calculations. Later I came across a post of Terry Tao "Write professionally", where (among other good things) he states:
"The standard format for mathematical papers is TeX, AMS-TeX, LaTeX, or AMS-LaTeX; other formats such as Word or Mathematica can cause technical difficulties (and will ultimately need to be converted to a TeX format), and so should be avoided."
The first thing I thought was "No way, I do not believe that somebody uses Mathematica for writing papers." I know a few experimentalists who submit articles in .doc format and are happy with it, due to lack of equations. But, as far as I know, using something but TeX is considered as kind of "mauvais ton" in math community (please tell me if I'm not right).
This post is not really about some disadvantages of Mathematica interface. But such useless options of notebook formatting as e.g. "Journal Article", "Preprint", "Report", "Book" and "Monograph" can inculcate a bad taste of writing papers in students, who may postpone learning TeX.
Nevertheless, as mentioned by Philip, Mathematica notebooks can be used to write up some daily results with the following data analysis. For a final draft it is better to use something else, though.