I was playing around and found a rather easy way to defeat the weapons.
Ruby: Equip knights-of-the-round and hp-absorb together. Also have a w-summon. Everytime you cast nights of the round you will cure yourself before Ruby can counter with Ultima. He will be a very easy battle!!!
Emerald: Same thing applies as above. It helps to equip as many of your characters with "sprint shoes" and "mime". This will allow your first character to cast two knights-of-the-round while curing himself, and since your characters will have haste automatically (sprint shoes), your next character can mime knights-of-the-round and likewise completely cure themself. This method works extremely well! I beat emerald like this with 6:22 still left on the clock in the corner. I only needed to use final attack-revive twice since he did use the Air Tram attack twice.
Good luck!