The Republic is a large body of government comprised by dozens of planets. Any organization this big is bound to have corruption. Some governments had more influence and more power than others. On the surface, things ran mostly in a smooth and fair manner, but if you looked under the table, there were underhanded deals being made and small planets were secretly suffering injustices at the hands of some of the stronger and less moral forces within the Republic.
This led, naturally, to discontent.
That is how the CIS, the Separatists, were born. They were an alliance of governments and institutions (Like The InterGalactic Banking Clan) that rose in revolt, wanting to separate themselves and create their own Republic, so to speak. As the war went on, the CIS and the Republic would both do terrible things, although the CIS was painted in a more darker light because of their employment of pirates, slavers and a force comprised mostly of unfeeling droids. Not to mention that the CIS had as much corruption as the Republic.
Is there a good and bad here? Not really. There was corruption in both of them. Both did questionable actions.
If you dont mind the spoilers:
The truth is that both the Republic and the CIS were played by Darth Sidious, the Sith Lord. He was disguised as a Senator of the Republic, and he wanted the CIS to rise to power and challenge the Republic in order to weaken it so he could take power. So he would play both sides. He would make the CIS strong, then he would make the Republic strong, then he would have both of them destroy each other, take over the Republic and use his agents in the CIS to take it down.
So yes, ideally, a status quo where neither the Republic or the CIS gets the upperhand is ideal. If both sides were equally strong, the war would drag out into a cold war and it would be possible to reach an agreement in the future.