I feel I get the gist of rarity for most things, except I'm not sure how it is supposed to work with Clerics. If I'm reading it right Clerics still get their full spell list to choose from when preparing spells. So how would you restrict rarity?
The first thing that comes to mind is by the deity they serve. So clerics of Sarenrae and Pharasma who have the Healing domain would likely get it as common. Maybe some others like Desna, and Shelyn that might have it in their domains or be likely to grant it more freely. But then any other would have to make an argument to their god why they should provide the spell to that cleric, or perhaps perform a task to earn that spell.
What are your thoughts?
Rarity does affect which spells you can prepare. From page 69: "At 1st level, you can prepare two 1st-level spells and four cantrips each morning from the common spells on the divine spell list in this book (see page 200) or from other divine spells to which you gain access."
So non-common spells in the core rulebook and all spells in future rulebooks are by default unavailable unless you pick up some character option that grants you access to them.
And make a Religion check and spend money to learn them.