HAHAHAHAHA!!!!!
I voted for....
Ultima Weapon!
I voted for him because he took me the longest/most effort to beat. You have to chase him around soooooooo much to kill him.
For Emerald and Ruby its more like yawn, KotR do your thing. Victory song. Party levels up a bunch.
Though this is just speculation. But I bet that if you were to add up all of the HP/MP from every time you fought Ultima (In Mideel and the 5 or 6 times when he's flying around) and added that to Ultima when you fight over Cosmo Cannon then He'd probably be A LOT harder to kill than Emerald. Maybe.
I mean you see him hovering over cities forming giant balls of blue energy. I bet that attack could kill Cloud. And Shadow Flare rocks just because its name sounds so awesome.