I have not experimented with Notebook styles, but from what I understand they can be customized to a wide range of styles. Is there a style which looks like a typical paper written in TeX/LaTeX?
My idea here is that instead of writing a paper in TeX/LaTeX, I would write it Mathematica using a LaTeX style, then just output the LaTeX encoding for the notebook and it would be ready for publication.
The biggest problem I guess would be with the plots. Most people seem to use PGF-Tikz, Gnuplot or PGFPlots to generate plots for their LaTeX papers, but if I use Mathematica, I guess I would just have to use an image output.