This is a very interesting question. Anything after IX doesn't exist to me, so thinking about this... given how FF battle systems are all roughly the same, they would all be about equal at Level 99 with access to any equipment in their game. Ultimately, I feel it would come down to being able to "game the system" with bugs, which leaves me with Butz and Locke. Locke's Vanish+Doom is effective against most things, but it takes two turns to use. Butz, on the other hand, could optimize his evasion and defense, then use Mix with Kiss of Blessing to nerf anything. With Guard and Counter as his other abilities, I think he could then be invincible against anyone as long as that works as I remember it and he can survive the first turn.
Of course, Zidane has Solution 9 and could one-shot any of the playable characters so long as he starts with a Limit Break.
Much to my dismay, Cecil would be at the bottom of the list. Tragically, anyone who isn't Kain, Rosa, or FuSoYa sucks at fighting in FF4. : (