I'd say Saturn too! he's my favourite member of any Team, he would dominate if he was in charge! I'd see him as the boss, Jupiter as his right-hand woman, and Mars his left-hand. I see Jupiter as the hottest, and her Skuntank is pretty tough, she is harder than Mars, but I just can't see her bossing around the entire organization.
You know, my first thought was Saturn, too. But then I thought more. (That's a big fault of mine.)
In Platinum, we see that Charon (I will always prefer Pluto) actually has the greed, ambition, and corruption to desire to continue Galactic's antics after Cyrus is dispatched. He even gets Mars and Jupiter to follow along a bit with his goals though they both seem to hate him. Of all the Galactic Commanders, I'd be willing to bet he'd be most likely to take over Cyrus's position.
Then, Saturn. Yes, he's pretty much the most competent and Cyrus's righthand guy, but... I can't see him actually taking over. We also learn a bit more about him in Platinum version, and it appears that he really doesn't want to control the team or do anything Galactic-ish to the universe. He starts philosophizing about ethics and meaning, if I recall correctly, and generally seems apathetic to Galactic's - Cyrus's, I should say - plans.
So I'll vote Jupiter. She seems ruthless enough to head an evil team. She was more rational and organized than Saturn and Mars, respectively, and certainly seemed to me to the most dedicated to Cyrus's actual goals than the other two (who appeared to merely be dedicated to Cyrus himself).
Mars just looked like an impetuous child to me. She couldn't lead the team anywhere other than The Gap, probably.