I think the newly setup wiki is currently a bit of a mess (though Eliminator and others have already spent time on improving
https://docs.megaglest.org/Mods/List - the page I assume you are primarily referring to). Omega did a great job copying all the content from Wikia to our new wiki, but we need yet to rearrange everything there now, update it, with a primary focus on MegaGlest.
Personally I think that factions should
always be wrapped up in a techtree, since that's the only way you can easily and cleanly install and use them. So existing single faction downloads should be repackaged to become complete techtrees (can be minimal, possibly based on a techtree template so that you just need to add the existing faction data and make minimal changes), and a copyright + license statement, description text and screenshot should be added. This way they'll be (almost) ready to go to the mods menu, too.
Single factions which have not been repackaged as a techtree, yet, should (in my opinion) remain on a separate list. I agree with you when you say that any readily usable single faction
techtrees should not be listed under "factions", but on the techtree list.
To make things even more complex, mods, to me, are not just the same as techtrees but can be any type of contribution which is in a format MegaGlest can use. Namely complete techtrees (consisting of one or more factions, resources etc.), scenarios, tillesets and maps. As such,
https://docs.megaglest.org/Mods/List should either contain all of these mod types under the different headings (but this would make the page huge, so I think that's a bad way to deal with it) or - preferrably - it should be renamed to
https://docs.megaglest.org/Techtrees/List or just
https://docs.megaglest.org/Techtrees and additional pages should be added for the other mod types, with links to these pages on the
Mods page (and no actual mods there).
Finally, we also need to track versions and point out which of these mods (and ideally which version of it, too) is currently available on the mod menu.