Currently, I'm planning to redo a lot of my homebrew setting after I've gone through the official PF2 rules (& made Character/GM Sheets).
For general areas/regions - I'm planning to make a masterlist of several rarities specific to that region which I can easily pull from & share with players when starting a new campaign.
For deities in particular, I'm planning to use rarity to help show where they're actually worshiped/known in the setting (my setting currently has 153 deities - though I planning to prune some & rename many of them). Hopefully this will make my very large list much more manageable.
For races & classes, I'm not particularly a fan of making players feel too restricted in their selections of these unless they're very specific to an area (such as Samurai not being in a medieval Europe-style region). As such, I'm planning to allow players to pick uncommon races/classes without needing GM permission - instead stating that picking an uncommon option here means that NPCs will react, often negatively, to the character if they are aware of their race/class. The player can try to hide this if possible (tiefling covering inhuman features, Witch pretending to be a bard/eccentric wizard) but there are consequences if they are revealed (such as certain areas making witchcraft a burnable offence). Basically using the tag here to preemptively warn the player that while they can pick these options - doing so can come back to bite them and they should be prepared/expecting such.
For spells, I'm planning to bump certain categories (long-distance teleportation, resurrection) straight up to rare to signify next to no one has access to them within the setting, and the ones who do aren't sharing for various reasons (Resurrection in particular damages an already fragile & pieced together afterlife system in my setting).