Have they become irrelevant now? Because I've been mucking around with some transferred pokemon today and found out that pokemon with mismatched abilities now retain its mismatched ability.
For example, I had 2 staryus palparked from Emerald, both with natural cure, however 1 of them was given the 1st ability slot as its PID while the other got its 2nd ability slot for its PID. Once I evolved both of them on pokemon Black, the staryu with the 1st ability slot's ability changed to illuminate. However, this time around in pokemon X/Y/ORAS, both Starmies retained Natural Cure.
Does this make the ability slot number irrelevant now? I'm guessing if it is, that this is due to the ability capsule item being released.