I've used TeX with eplain and for many purposes it's great, but publishers and coauthors essentially mandate LaTeX for real papers.
Pollen is intriguing[1,2], but way too early to say anything about. If TeX or LaTeX are going to be displaced any time soon, it's going to be because of textbooks published on the web (caveat: unfounded speculation on my part, but read on). I'm sure it's possible to embed a dynamic simulation into a pdf, for example, but nothing like what can be put online. And LaTeX isn't designed to produce websites.
The power of TeX is that it is a powerful and beautiful type setter. Something like a website was not on the horizon.
For Online-Documentation the best option for me is Sphinx at the moment. It is extendible and still a clean markup, slightly more powerful than markdown but does not get into the way.
It is no coincidence that it uses Latex for generating its PDFs. Sadly its not possible then to polish the printable output in the same way as you would be able in tex or latex.
Pollen is intriguing[1,2], but way too early to say anything about. If TeX or LaTeX are going to be displaced any time soon, it's going to be because of textbooks published on the web (caveat: unfounded speculation on my part, but read on). I'm sure it's possible to embed a dynamic simulation into a pdf, for example, but nothing like what can be put online. And LaTeX isn't designed to produce websites.
[1]: http://mbutterick.github.io/pollen/doc/
[2]: https://news.ycombinator.com/item?id=7822057 (HN submission)