As a plot point, we always knew the Clones would win. They had to. The CIS couldn't win at the end of Episode 3...unless the Storm troopers in 4-6 were secretly droids ^_^
What am I talking about, is the vast outclassing of the CIS versus the Clones.
Lets look at the advantages of each
1. More flexible and can innovate with more frequency and success.
2. Better Leadership, (mainly costing of the Jedi on the ground fighting along side of them).
1. Vastly Superior Numbers
2. Greater Coordination and ability to adapt to changes on a widespread level faster then Clones
3. Superior Armament
4. Superior Logistics (Troopers are cheaper. Do not require food, or aid. Meaning more troopers and ammunition per deployment)
5. Ranks can be replenished quickly.
Even with the great benefits of the Jedi, the Droids have the clear advantage. They are more heavily armed, overwhelming numbers, and superior logistics.
The only true logical factor in how the CIS could lose (aside from making the plot work ^_^) is the Sith i.e. Palpatine.
But here in lies the problem. Palpatine's goal is to gain control of the 'republic' (read Galaxy) and destroy the Jedi. It doesn't really matter which army he supports, he would still gain control, no matter who wins.
The Clones win, he gains the respect and love of the Senate and they convert into the Empire.
The CIS wins, he gains control of the dominant military and economic force in the Galaxy.
It's win/win scenario for Palpatine. So it seems to me, at least so far, that the only reason the CIS loses is merely to fulfil plot points for the series. :O