Something I noticed the last time I played through--

After fighting Ultimate Weapon in the crater near Junon in disk 2, he flies off in some random direction and you have to crash into him until he starts flying strait towards one of the reactors in the world. After defeating him at the new location he disapears and you have to scour the entire world to find him again. I thought he appeared in a random location at first, but it seems he returns to the crater near Junon each time you defeat him and he starts flying around from there. So after each battle rush back to Junon quick enough and he should be around there somewhere.

I'm not 100% sure if this is correct, but It worked for me. I remember the first time I played the game, this quest took me over an hour to complete - using this method it took about 10 minutes.