Omega's pretty hard unless you use Magic Sword with Bolt3 and X-Fight. I'd say Shinryu is even harder, though. It has tons of attacks that can really slaughter your party. It also has a lot of HP, and there's not a really easy way to kill it as far as I know. You have to beat it the hard way, with raw firepower and one major battle. (SPOILER)Neo Exdeath is also quite hard if you're on lower levels, but my vote still goes for Shinryu.

EDIT: By the way, who's Averis? And is "Gilgame" referring to Gilgamesh or Gil Turtle (I think it was called Gil Game in some translation)?