As surprising as this is, I think Mojo Jojo could win. Let me remind you he's a genius capable of creating high tech weaponry which he could conquer the world with hadn't it not been for three super-powered girls who fight giant monsters on a basis and shoots lasers with their eyes.
Koba is tough, but Mojo has a big advantage here in sheer weaponry. Though if it were without weapons, Mojo would f*cking die.