Yea Ultima and Omega aren't in the arena so you won't find them there. They are down in the Zeritan Caverns(sp?). The arena boss that is the hardest has to be Nemesis, even with my party over 25,000 HP each and inflicting 99,999 damage each he still gives me a hard time.

Storyline boss I have to agree with Josh R, Seymour on Mt Gagazet gave me a hard time when I faced him the first few times. The other boss that gave me fits was Yunalesca in Zanarkand.