Who would have won the clone wars?
If palpatine never sounded order 66 or anakin was never sent to operation knightfall or became palpatines apprentice and palpatine was killed by windu but the sepratist council was still living. Who would have won the war? The republic or CIS so far it looked like the clones where winning
The CIS was on it's way out by the time O66 happened, pretty much.
Once Dooku and Grievous fell, the CIS lacked a strong military leader. The Republic had more resources, and while the Separatist council was still around, they were political and economic leaders who couldn't run the hit-and-run war (Grievous) or propaganda war (Dooku) without their leaders.
Things would've dragged out more without Anakin being given their location by Sidious and allowed to wipe them all out, but the Republic would've either found them eventually and some other Jedi would do the same, or the factions would be taken down piece by piece.
Originally posted by Lord Stark
The CIS with competent military commanders across the board would defeat the Republic.
Not by the late war, the CIS had some innate disadvantages, namely total territory size and quality of troops.
Early on the CIS had a significant edge, the Republic didn't have an army ready and they lacked the operational experience with war. Later on, the Republic's larger number of worlds gave them the industrial edge and the ability to make larger fleets, and additionally the clone troopers benefitted from experience more than droids did. The ability to crank out super-cheap troops ultimately doesn't make up for that.
There's a reason why Grievous retreated so much, and it wasn't cowardice- His job was to preserve the CIS's fighting strength while inflicting what damage he could. Pitched fleet battles against a foe with more worlds would've bleed out the CIS's strength fast.
That's also why he went for high-risk moves like trying to capture the Grand Chancellor from Coruscant in the middle of enemy territory. It was a blow that could potentially severely affect Republic morale (and note it was a kidnapping, not an assassination, which would only serve to harden the Republic to a longer war), but it also risked a lot of forces on a move that didn't have to do with taking or defending territory.
The CIS basically needed to win quickly, find some other way to force a surrender, or they'd lose the strategic resource game.