Well the CIS may have won without any interference, in short they were all tricked by Sidious/Palpetine and then slaughtered by Anakin, who is left to lead them now? Sidious/Palpetine obviously is the only one left, and since he controls the Republic as well and has dissolved a large portion of the senate, well now he controls the whole galaxy. It's not at all that the Republic beat the CIS, it's that the CIS was betrayed from within and all were slahed down by Anakin. If we were strictly talking a war with no one playing/controlling both sides and such then the CIS would of probly won, they had greater numbers in troops and they were fairly popular among alot of systems. If you really think about it, the CIS turned out to be the true good guys, since they were fighting to end corruption(yes I know they had evil tactics as well and such, but it's war) in the senate and the galaxy and be a true democracy, while the Republic turned out to be the oppressive empire that we all know from the orginal movies.
quote from wookiepedia about Sidious/Palpetine
"During the Clone Wars, he was the secret de facto leader of the Separatists as the Sith Lord Darth Sidious, as well as the de jure leader of the Republic, allowing him to plan and execute the entire war, thus resulting in his ultimate triumph with the rise of his Empire."
One thing so great about the SW saga is the fact that alot of details are left open to interpretation.