I'd say Ruby is by far the hardest. Emerald is just a push over, once you know what you're doing and/or have Underwater Materia. And, Ultimate...... WHAT ARE YOU KIDDING ME!? He's the easiest of all the bosses in the game.... except for the final, kill him with omnislash, sephiroth, I guess.

P.S. please don't make a big deal about my, Ultimate being the easiest, claim. I was just trying to make a point.