As long as we're talking Legendary Abilities, let's mention
Pressure. Because there's no logic there. It's sort of the default, this-is-a-legendary ability, being on EVERY non-mythical from Gens 1 and 2, and several from 4. But Deoxys is the only Gen 3 legend to get it, and Kyurem-Base the only post-4 Legendary with it. Meanwhile non-legendaries that get it are Aerodactyl(probably a reference to the Legendary Birds), a few powerful/rare/weird mons like Absol and Wailord, and then stuff like Dusclops and Bisharp chosen seemingly at random. I'm just not sure what they were going for. If it's just supposed to troll you by making captures harder, why didn't they use it for ALL legends*? But if it's supposed to represent fighting an overwhelming opponent, why do any of the random mons that get it do so?
*Yes, Kyogre/Groudon had reason not to get Pressure, but the Lake Guardians, Regis, Swords of Justice, etc would have made perfect sense with it