That's not manipulation, that's waiting for the right moment to strike. The emperor was already an evil and ambitious man who wanted the power of the Espers(and the Triad) and went after it. Kefka didn't influence/manipulate Ghestal to be that way, or to do those things.
Also, both times Kefka and the emperor pull a bait-and-switch on the party, the credit for the idea/plan is allways given to Ghestal(by Kefka himself no less).
In the end, Kefka just went along with the emperor, following his orders and plans, while waiting for the right moment to strike. There was no manipulation.
Kuja on the other hand actually manipulates people. Brahne is after the Eidolons like a power-hungry bitch because of him. He summons Bahamut at Alexandria, knowing that it would force Garnet and Eiko to summon Alexander(permiting Kuja to take control of him through the Invincible, his plan all along), therefore, manipulating Garnet and Eiko.
Sorry, but Kuja seems smarter to me.