Here's some insight for you
The CIS was INDEED meant to serve as a 'backup plan' for Sidious. It's actually perfect how good a plan it is to lead the CIS into a war against the Republic- he could easily 'tip' the sides either way.
We know Palpatine controlled both the Republic and the CIS, and he meant for the Republic to win.
However, the CIS was a security measure for Palpatine.
Think about this: If the Jedi Order discovers the identity of Palpatine as the Sith Lord AND the leader of the CIS, EG 'his worst nightmare'...NOT.
Palpatine doesn't have to give two hoots whether the Jedi discover him, because as long as he can RUN away from them, he can rejoin the CIS as Sidious and lead the CIS to rule the galaxy.
As Chancellor he knows ALL the operational secrets of the Republic, and as master of the Clone Army, he still has control over the clones. Order 66 is possibly..one of many possible orders. He probably has a 'kill switch' for the Clone Army as well.
So there's two scenarios that Palpatine has thought out.
-The one that worked, the CIS exhaust the Jedi and he betrays them, leading the Republic and terminating the Jedi
-The Jedi find his true identity, and Palpatine rules the CIS as his Sidious persona. They don't care that's he's a Sith Lord, they knew that already, and he controls all the droids anyway- they have no choice in the matter.
Mace Windu was VERY right when he tried to kill Palpatine. There is pretty much no way to stop his plan short of killing him. If you tried and imprisoned him, he would have 2 loyal armies that would attempt to break him free and dissolve the government.
The only other possible scenario where the Jedi win if Palpatine is allowed to live/flee, is that if they somehow escape the destruction of the Clone Army, raise a normal army from the galaxy's population, and fight the Emperor that way.
And that's EXACTLY what they did in terms of the Rebellion. Except you know, I'm guessing they didn't plan to have only 3 of them left.
Edited by TarlSS, 02 April 2014 - 02:45 AM.