Do not use physical attacks on Omniscient. Only do that if you are near death and cannot heal anymore. If you do, he will cast Return, resetting the battle. However, Omniscient is otherwise very easy. You can prevent him from casting anything by attacking him with a weapon previously enchanted with Silence.
The best method is to cast Carbuncle, so you reflect all his attacks back at him. Another method which is also pretty humorous is to cast Berserk on him and summon Golem. This way, he cannot use Return to restart the battle, and you will not suffer damage from his physical attacks. When he dies, he casts Flare, but provided you still have Reflect on your characters, or he is berserked or silenced, there should be no problems.