This question has been going through my brain for a while now, so I'm curious what other people think.
In the Original Trilogy, the Rebel Alliance who are the "good guys" are sabotaging the Empire's efforts and trying to cause destruction from the inside. Using violence, the Rebel Alliance finally manages to gain independence from the Empire and become the New Republic. They based their entire war on principles of government and used violence to support their fight.
Now rewind twenty or thirty years ago, to Episode II. Several systems are upset about how things are being run in the government and so want to peacefully leave the Republic. However, they meet stern resistance and when they try to execute some spies who are illegally infiltrating and killing some civilians (Obi Wan, Anakin, and Padmé), the Jedi Order begins a massive attack in order to free them. After the CIS tried to put down this invasion, a full-scale Republic invasion of Geonosis begins which leads to the Clone Wars, justified only by retrieving three important people.
Frankly, I think the CIS were much more justified than the Rebel Alliance was. It seems that who's good and who is bad is based upon whether or not you believe in Jedi or Sith philosophy. This also forms a strong parallel to the American Revolution and Civil War now that I think about it, however the North had more reason to fight than the Republic did, namely because the Republic is very corrupt at this point.
So, post your thoughts and comments about who was morally justified in these wars, and don't just say someone was good or bad because George Lucas wanted it that way. Thanks for non-troll responses.
the original trilogy is a direct parallel of the Imperials - Great Brittain and the Rebel Alliance - USA, so answer your question yourself with that in mind.
but in the movies, the Imperials are right in both cases, prequel and later, the the whole war is caused by the jedis need to eradicate the sith (not the other way around mind you), the whole war was fought and lost by that case alone, very lame imo since the jedi code is a lie and the sith code is something we deal with on a day to day basis in the real world...