If I honestly had to say which I had more trouble with, it would be Ruby. With Emerald, if you know when his eyes appear and that they only have 25'000 HP, the fight is already over. Stack up a W-Ultima and a Slash-All when they do appear and you're back to square one immediatly. You never even see any Aire Tam Storms. Regen does all the healing you'll ever need and then just cut him to death. 4x Cut speeds things up tremendously though it's not really necessary.

With Ruby I simply didn't know what character would be left standing two rounds into the fight so I had to equip everyone properly for the chance that they be the one. This was also the fight where I realized how great Hero Drinks are in this game. Since the character left standing had Enemy Skill and 4x Cut, it was only a matter of time until I won.

The reason I put Emerald instead of Ruby into my Top 5 was because I think Emerald Weapon is just a more well-designed boss. Ruby is a bit like Major Numerus in that it feels not that much thought went into him. He has a bunch of attacks that deal a bunch of damage, he has a ton of evasion, defense and HP. And well, of course he ejects two party members, but that's basically it. You don't really have to go far out of your way to defend against any of it. Emerald can trip you up quite a bit.