I agree the GH wiki is limited. I think for content indexing and classification Sphinx/ReadTheDocs could help.
However the tool is not enough. Keeping the site structure clean and coherent requires a dedicated team of people with shared goals.
So what I really like of GH is
- Markdown (Discourse) and RST (manuals) format support
- Collaborative content workflow and discussions
- New organization privileges handling, allowing better team support
And this is my vision. We're now using 4 sites/platforms:
- www/Wordpress
- docs/GitHub (considering readthedocs.org as just the "docs viewer")
- community/Discourse
- dev/Redmine (and GitHub also)
I think it would be good if they'll be just 2!
- Discourse/community (with Markdown format)
- GitHub based:
- docs (via RTD.org),
- dev (via waffle.io, Taiga.io...) ,
- www (GitHub pages, Jekyll, ...)