Crystal WEAPON is the hardest of them all!! (Crystal is the one that (SPOILER)got its head blown off by the Junon canon)

No, seriously, I'd have to say Emerald. That Aire Tam attack causes you to equip minimal materia (so long as you know why), and because of the timer, you have to equip at least one materia, Underwater (unless you do that limit mime trick to defeat him in under 20:00min.). I think Squaresoft intended Emerald to be harder, which would be why you get the awsome prizes after beating it, but after beating Ruby, the only prize you get is a crappy Gold Chocobo (not good for races).