Emacs' Org-mode is pretty good for writing articles. It can be configured to use whatever package / setting one wants while exporting to tex / pdf, e.g. use some .sty files (presumably, I haven't needed them yet), or use the beamer class to make a slideshow. It can be integrated with the ESS package so that it can be used as a live programming environment for R, or whatever else the package supports. And it also supports todo lists, agendas, and any sort of note-taking from the first moment.
Example config for latex export (although I do not write academic articles):
I would highly recommend org-mode for writing documents and papers. I'm an academic, and have been using org-mode for the last 4 years as part of the paper writing process.
One of the best features of this pipeline is the fact that I can write a large chunk of the document whilst conducting research. I can jot down notes, caveats, schedule TODO items etc. and just tag the bits I want for my own reference as 'noexport', so that they don't make it into the exported tex or pdf document.
Another great feature is that I can embed code for producing tables/figures all within the document and specify whether I want the code or result or both to be included.
Finally, once I am happy I have most of the document the way I want it, I export to tex to deal with the final tweaks to finesse things -- spacing for the entire document, fine-grained adjustment of figure formatting.
This ensures that I have all the information that went into constructing the document and allows me to deal with various venue-specific constraints like submitting a source archive, or pdf as necessary.
Here are some resources for getting started with this:
I wouldn't recommend org-mode for writing professional documents. It is more unstable than any other major piece of software I've used. I use it daily, but not for writing. Things get changed in each release, the documentation is rarely in sync, and in a lot of cases major changes are not documented at all.
I learned the hard way. I wrote some presentations using org-mode. Then they changed the exporters without updating the documentation. It would be especially problematic to write an academic article in org-mode, because you might have to return a year or two later, and that's not when you want to find out how much has changed since you last worked on the paper.
One can keep the intermediary .tex files should they export to pdf. Or for any substantial project one can fix the version of org, as other projects do so with the versions of the compiler or of the libraries. Still, if you are correct, then it is a problem for every user. I haven't encountered such problem in my use, although my use of ox-latex has been rather superficial (some homeworks, a tiny CV).
It's true that org-mode is a bit of moving target, but the basic syntax for document formatting doesn't change. If you are really worried about this you could record/archive which version of org you used to put your paper together.
Example config for latex export (although I do not write academic articles):
https://github.com/cadadr/emacs.d/blob/c81ff8afa3ca4ab553013...