Garland ruled over the sterile, unchanging precision of Terra and its confined souls. Kuja, however, was made to be adaptable and destructive in the chaotic wilderness of Gaia. Garland was more powerful in terms of sheer force and will, but Kuja had encountered challenges, forces and emotions during his time on Gaia, the likes of which would not have been imagined by Garland. Garland deals in absolutes: straightforward solutions to straightforward problems. 'If Kuja's malfunctioning, send someone to kill Kuja.' When lateral thinking is required, he 'passes the buck' by delegating the resonsibility. 'Kuja's out of control in an unstable world, create someone adaptable who can counter this threat.' This seems to be the rationale behind Garland's creation of Zidane.

So, back to your question... Who would win if the ultimate battle was fought between Garland and Kuja?
Garland's been very powerful sincce the Terrans created him. He's aware of what he's capable of, and has the arrogance which accompanies that knowledge. Kuja's potential is untested. His emotional attitude gives him access to 'Trance', a source of greater power which Garland couldn't unleash. Kuja has had the time and ability to grow, learn adn become more powerful than he originally was.
Kuja would, most likely, win - in my opinion.