In a way, Ultemecia was the Main Enemy all along. How, you may ask?
Simple; Edea was possesed by Ultemecia. Then when Edea was freed and back to the Matron that she was, which is at the End of Disc Two, Ultemecia is introduced to everyone. Although she was in the bad guy business from the beginning. Also, Stupid Moomba, if you think Ultemecia popped up a little too late, what about Necron. all though he represents life and death, he just popped up at the end, just like that.
I rest my case.