What if...Kuja was the main character?

Well, then the roles would be reversed, naturally...
Instead of saving Gaia, the player would be trying to preserve the souls of Terra by influencing the cycles of life on Garnet's world. Still arguably a 'noble' goal, but from a different perspective. Then, of course, Garland -and consequently Terra itself - become the enemy too, leaving Kuja battling alone against everyone in his quest to (1) steal eidolons and (2) destroy everything.

What if...Vivi was bad? Then he'd have to be spectacularly more powerful in order to be a decent boss. No, seriously, it'd make a huge difference if he had that same natural malice as the Black Waltzes. He'd be confident and angry in spite of his limited size and power, instead of shy and afriad for those same reasons. He'd probably be a bit like Black Mage from 8-Bit Theatre...

What if...Queen Brahne was good?
In a way, she was. She was simply manipulated by Kuja... but if she was truly good, then she'd never have gone up against Cleyra, Burmecia, Lindblum and her own daughter. Kuja's job would've been a lot harder. He would've had to try to influence one of the other world leaders to start all the necessary wars.