It was all about the Jedi, if the whole Jedi Order had been organised to fight an obvious threat (such as the CIS) their enemy wouldn't have stood a chance, as it was they had no idea who the real enemy was until it was far too late for them to do anything. Also, its far easier to control people who supported your rise to power, so Palpatine would have wanted the Republic to 'win' because it would then be easier to control the galaxy. If the CIS had 'won' then a rebellion would have sprung p much earlier.
"Good and evil are but points of view. Many would call me evil for the things I have done, but to myself and to my followers, I am the saviour of the galaxy. I have not shirked from my duty because it is unpleasant or because others will disapprove. I regret the deaths I have caused on this path, but they were necessary to prevent far greater evil. So, Jedi, who are you to say what I do is wrong?"
-Darth Xenus, Emperor of the Sith