It is a known fact that there are two possible slots for Hidden Abilities, the second is simply not utilized. So this allows us to use that slot for the species.
What purpose would this serve?:
- In each generation there are new abilities introduced that can be utilized by existing Pokémon. For example, Strong Jaw can be utilized by Shinx and canine Pokémon, but there isn't any that gets it.
- In addition to this, several Pokémon have completed their slots with largely worthless abilities, so this method provides them access to at least one amazing ability.
- What's more, currently Ability Capsule is worthless for HA Pokémon. Having two slots of HAs provides an easy way of solving this issue.
- Some of the abilities that flavour-wise useful can also be granted to existing Pokémon. This has been the case for some of the HA distributions.
- Of course, some of the lost abilities can also be brought back, like Shadow Tag for Litwick and Quick Feet for Scolipede.
How would these be available?:
The same method how regular abilities are available. If an encounter has a chance of having its HA, then the HA of the species you encounter is chosen randomly from the two available slots. For example, the Shinx you encounter in the horde can either have Guts or Strong Jaw.
As for the breeding methods, the same chances of getting the slot would apply in addition to the chance of getting a HA at all. So for example, you would have %48 chance of having the HA your parent has, %12 chance of having the other HA, %20 chance of having regular Slot 1 ability and %20 chance of having regular Slot 2 ability(Note: %60*%80=%48 chance; %60*%20=%12 chance. %80 is the chance of having the ability slot your parent has and %20 is the chance of having the other).
How would these be distributed?:
Unlike the primary HAs, the secondary HAs would have to be distributed to Pokémon that already gained three Abilities, as they are the ones that require updates, whereas others can have existing abilities or new retconned abilities retconned as one of their primary or hidden abilities.
Similarly, since one can get only one Legendary per game, Legenderies can't have secondary HAs, much like how they can't have regular secondary abilities.