Lv.99 chocobo isn't a "rare game" per se. A rare enemy yes, but not from the category rare game. I never fought one, though I tried to spawn one at one point, unsuccessful as you can guess.
Anyway, from all the official 80 rare game, the hardest for me will always be Disma. Not only does it only have 5% of chance of spawning, for some lovely reason, everytime I play, he always spawns on my first visit to his place and won't be gone till I do kill him (he's one of those that gives trophies, if I remember well, and for that, I'm glad). Disma literally starts obliterating my party easily, and with all the other undead around, it's hard to keep alive with the constant hoard of attacks.