I've just suggested below, in the subthread started by facetofcathy, that "Fandom by Source Community" might more properly be labeled "Fandom by Community". It seems to me that this may address the problem with "minority fandoms" by removing size (and thereby the implication of hierarchy that goes with sorting things by size) as a necessary component of the concept of community. To reprise the statement I made below, if one is going to be non-hierarchical, one should be non-hierarchical in all directions at once.

In this context, skaredycat's comment in the same thread, about Categories in the wiki context becoming more like tags/wuzzles in AO3 context strikes me as thoughtful and perceptive. Essentially, we want to give the user the ability to sort things in as many ways as possible, and the trick in accomplishing any proposed restructuring is simply to avoid losing various existing ways to sort things in the process.