I was wondering what constituted the removal of categories such as Moon, Intended, All Unique Pearls, etc. Thank you!

Moon% was replaced by Cloak Retrieval, more or less. Similarly, Intended route was replaced by Story. Not hard set rules as the current categories are just a guess from shortly after Downpour releasing instead of based on demand.

We can always add more Misc. categories if there is interest shown (at least 3 people do a run of it), and there are enforceable rules that the mods can actually approve. That's how most of the Misc. runs were created in the first place.