Omega (FF8), Ruby, and Emerald all require preparation to overcome, and not much more. You have to be prepared in different ways for Omega and FF7's Weapons, and it's not easy to determine which Weapon is most difficult. It definitely takes more preparation to beat Ruby and Emerald, so by that line of thought, I suppose they're more difficult.

I found Ozma from FF9 to be a more challenging fight then any Weapon, though.