Merton + Fire absorbing equipment is the BEST thing EVER to do in the fight vs. the Goddesses and Kefka. I mean, 9999 damage + your characters healed!
But Ultima is more useful at other places in the game, where enemies have various elemental resistances. Try going up on Fanatics Tower (or was the name Magic Tower? Where you find Strago anyway...) without Ultima, it's really hard.