Just kill the characters that Ultimecia picks until you get the ones you want. Then summon Cerberus and Doomtrain, triple cast Aura, and spam Limit Breaks. This strategy will defeat EVERYTHING if you have the right junctions.

If you're going for the optional "mega bosses" Ultima and Omega, definately shoot for Lv. 100. Equip 4 Plus abilities and go straight to 100 to give your characters a good stat boost.