I dunno, I tend to say the Alliance.
Barring Dooku or Skywalker in battle, it would seem the Alliance would be stronger.
The foot soldier battle droids are useless. I know the CIS has great battle ships, and mid-size attacks droids, but they were beaten by the Republic(translate:Empire), and the Alliance managed to gain the victory(ultimately) against the Imperials, despite being outnumbered, undertrained, and going against AT-AT'S, star destroyers, the death star, etc....
I would place my wager on the ever-resourceful alliance.
The CIS terrorized the Republic for three straight years of constant, head-on, warfare, not the sneaky hit and run tactics of the Rebels.
Remeber, the Rebels were ALLOWED to know the location of the DS, they were allowed to get as far as they did. Controversial as it is, if Palps hadn't died so timely, and if the Star Destroyers engaged the Rebels straight away, then the Alliance would have been finished.
Since this is a case that a MUCH larger fleet of only slightly older design is going up against the Alliance, then I doubt the CIS would lose. Luke wouldn't make a difference, he couldn't contend with the CIS Baddies.