i dont know why, but i say the confederates as the good guys in this movie, except Dooku of copurse, cause if the confederates won, there goverment would have to better then the empires. well, then again, im an idiot, so let the flames begin!

In a way, the Seperatists are the good guys... they just want to be free of the corruption of the Senate.

However, you hafta realize that the Seperatist movement was originally orchestrated by Palpatine (by way of Dooku) in order to get him Emergency Powers in the first place.

All part of Sidious' grand scheme... :D