Even without Thrawn the CIS would have won the war if it weren't for Sideous playing both sides, due to their overwhelming logistical advantage. So if Thrawn was in the game it stands to reason that things would have played out the same. Any advantages Thrawn gets would be sabotaged by Palatine.
The cool X factor to think about is that Thrawn might be smart enough to deduce that the CIS is being played by Palpatine, Dooku and Grievous and try to wrest control of the CIS from them. But in the end I think he would end up just getting assassinated by one of the dark Jedi.
I assume that if the CIS had won, Sidious would still activate order 66 to have the clones kill as many Jedi as possible. But even if most of the clones were dead, the remaining Jedi would still be f*cked against the CIS army, especially without clone reinforcements.
Then Sidious could just wipe out all of the senate members. Perhaps call a mandatory meeting to the senate chamber, and just bomb the entire thing.
Originally posted by SheevThe droids don't follow Palpatine they follow Grievous, who believed in the Separatist cause wholeheartedly.
But even if the CIS had won, they would have still just been consolidated into his new Empire.There was literally no reason for Sidious to care which side came out on top, when he controlled both. No matter which side lost, he still won.
Something to remember is that Dooku was the only high-level CIS member who knew that Palpatine was Sidious. If the CIS discovered that Sidious was not only their mortal enemy Palpatine, but that he was also planning to become dictator (something the space-libertarian CIS would ideologically oppose), they would have rebelled immediately.
tldr palpatine had absolute control over the clone army, he did not have absolute control over the CIS.
The CIS winning the war would have still left the galaxy at large split between two factions, which was counterproductive to Palpatine's larger plans -- he wanted absolute control over the entire galaxy. The Republic had already granted Palpatine an unprecedented amount of authority during the Clone Wars when he was Supreme Chancellor, and willingly granted him unlimited authority when he rose to the rank of Emperor after the war... Then it was just a matter of killing-off the remaining CIS figureheads and deactivating the droids, which was a fairly simple 'transition'.
On the other hand, trying to rebrand the CIS into a galactic totalitarian regime would have been a much more difficult task.
Originally posted by Sheev
Because the CIS could just usurp the position of the republic all together. The entire galaxy would be under the control of the CIS.
But that's not the goal of the CIS. They never sought to conquer the galaxy, just break away from the Republic. Destroying and replacing the Republic gov't, especially with a more powerful one, is the exact opposite of what they want.