Midgardsomr ran away from Omega, and Omega was responsible for imprisoning Primal Bahamut.

Koryu was so powerful that even with 4 Auspices and the Warrior of Light, it was deemed preferable to seal him away rather than fight him.

So I'd place my bets on Omega and Koryu as the strongest beings in the setting (besides possibly Hydaelyn and Zodiark, though we have little context for how powerful they were).