Star Wars has always been about allegories for real life wars, with the Original being more or less World War 2 in space and the Endor part of Jedi being Vietnam (at least that's what I've heard). Now it's easy to see how the Prequels are an allegory for the American Civil War, however if you think about it, apart from the few Jedi generals for the Republic and a few Confederate generals, it's the Republic which is evil and the Confederacy which is good, and here's my case:
1) The Republic made the war necessary.
With the source material seen within the movies themselves, we are shown that the worlds which seceded did not want to do so, but where given no choice. A bureaucracy as large as that of the Republic (governing over a million or so worlds), it's understandable that there are problems in efficiency and corruption, especially when the senators representing worlds on the fringes of the Republic have to contest with all the other senators for time with the senate's attention (the amount of time we see The Naboo has on the floor shows that there are worlds which are considered more important then others for this limited time). What we are shown and told is that these world tried to negotiate reforms which would be needed for them to function properly, to be able to prosper as the inner worlds which where getting more attention and priority in their problems being solves. And the Republic's reaction? The Military Creation Act.
2) The Confederate army of droids and fleet was a deterrent for war, and was not meant to be used.
The incident at Naboo in Phantom Menace showed the Republic it needed a military, and the creation of one at a time where the Republic was about to split into two made the breakaway state need to have one if it was to not be conquered in an instant. It was out of necessity that the Droid Army and the Banking Clan's fleet went from small forces used to police the trade lanes to a full military, it was in response to a nation with a larger economy and greater manpower threatening the creation of a military. It may not have been the Republic's intent, however it was an act that was logical from the separatist's perspective.
3) The Republic attacked first.
By the start of Episode II, the Confederacy is a de-facto state already, in the proses of homogenizing its political and economic structure from that of a breakaway into a real state. At this time there is no war, and there may even have been some low level relations between the Republic and Confederacy, or at the very least worlds within both (the enclaves of both in each other's territory without there being official war makes this very likely). So what else was happening at this time? The Republic was talking about creating an army (with the official opposition party being against it, though what the opposition was beyond The Naboo and Alderan is never stated), and the Confederate Droid Army made for their defense. And what was it that started the war, an attack on boarder worlds? An incursion into the Inner Core? An attack on the capital itself? No, it doesn't come from the Confederates at all. It's the Republic which starts the war, with an Incursion turned all out invasion of a Confederate world, which had been unprovoked as the only justification was the production of a fully justifiable army.
"But wait", you might say, "the Confederates started it with Jango Fett, who lead Obi-wan there". Well, the problem with that is, Fett was a private actor, which means he's the problem of whoever's territory he is in. When Obi-Wan was following him in his investigation, he was in Republic territory, in which he had the authority to do so, however, after he entered Confederate territory, his authority vanished because he was in another state, and was there illegally, so his actions where at best an illegal act and at worst the precursor to invasion.
4) The Confederacy was the underdog the whole time.
Now, when looking at the 'official' numbers of soldiers (which are wildly different depending on how one looks at them), one would think the Confederates have an advantage. After all, they have more droids right? However, the bulk of those droids where cheap worker units given a gun and sent into battle (the main battle droids where clearly created with cheap labor as their intent instead of combat, unlike the expensive Droidekas), and coupled with the manpower and economy the Republic had behind it compared to the Confederacy (up to 100 to 1 depending on the source), then it's clear that the best they could hope for was for their own independence to be secured. Just look at Coresant and the other Inner Worlds we are shown in Revenge of the Sith, they are not ones in a full wartime economy, they are clearly in a peacetime state with an active nightlife and a casual attitude towards even the war itself. "Oh, there's a war? I didn't notice. Wait, you can see the fighting in the sky? Well, the planetary barrier will stop everything. Might as well watch and enjoy the show". If the Republic was ever in serious danger of loosing, there would have been mass conscription and rationing of resources. Instead the bulk of the Grand Army of the Republic (another Civil War namedrop) is, for the most part, clones, as is the Navy, with the rest being local planetary security forces (which are glorified police, as we saw in Phantom Menace). Not that's all well and good, until you also realize...
5) The Republic uses slaves, and lots of them.
The clones are slaves. That's it. They where created to fight for the Republic, and no one cares what they have to say on the matter. They are shown that they have hopes, dreams, aspirations of their own. They give themselves names to replace the registration code that is used for identification, they give themselves unique haircuts to make it easier to tell who is who, they have different dialects which they use for casual talk, and it's likely that they have all manor of mannerism that are different from each other. They are sentient, self aware, intelligent beings who are indistinguishable from other humans within the Republic, and how does the Republic treat them? It forces them to fight against their will against an enemy they don't know for a cause they don't believe in. They don't want to fight? They never wanted to fight? Insubordination. Your rights? Sorry, not my problem. We never see a clone or two on leave, we never see them flirting with the local girls as real soldiers do, all we see is them fighting. And what happened when the war ended, did those who stopped wanting to fight get to? No, they kept doing their job as the army of the Empire. And when their creators tried to use them to rebel, then what? Then they took the most loyal, best of the best soldiers, and then committed an act of genocide against the remaining clones.
And so there you have it, the Republic man take many names from the Union's side of the Civil War, and many attitudes, however they where the evil ones, the ones using slaves. The ones who took the only hope that a large part of the galaxy had and smashed it to oblivion. And we are supposed to think of them as the good guys only because a few of their leading military where good people and a few of their opponents where less then honest.
1) The Republic made the war necessary.
With the source material seen within the movies themselves, we are shown that the worlds which seceded did not want to do so, but where given no choice. A bureaucracy as large as that of the Republic (governing over a million or so worlds), it's understandable that there are problems in efficiency and corruption, especially when the senators representing worlds on the fringes of the Republic have to contest with all the other senators for time with the senate's attention (the amount of time we see The Naboo has on the floor shows that there are worlds which are considered more important then others for this limited time). What we are shown and told is that these world tried to negotiate reforms which would be needed for them to function properly, to be able to prosper as the inner worlds which where getting more attention and priority in their problems being solves. And the Republic's reaction? The Military Creation Act.
2) The Confederate army of droids and fleet was a deterrent for war, and was not meant to be used.
The incident at Naboo in Phantom Menace showed the Republic it needed a military, and the creation of one at a time where the Republic was about to split into two made the breakaway state need to have one if it was to not be conquered in an instant. It was out of necessity that the Droid Army and the Banking Clan's fleet went from small forces used to police the trade lanes to a full military, it was in response to a nation with a larger economy and greater manpower threatening the creation of a military. It may not have been the Republic's intent, however it was an act that was logical from the separatist's perspective.
3) The Republic attacked first.
By the start of Episode II, the Confederacy is a de-facto state already, in the proses of homogenizing its political and economic structure from that of a breakaway into a real state. At this time there is no war, and there may even have been some low level relations between the Republic and Confederacy, or at the very least worlds within both (the enclaves of both in each other's territory without there being official war makes this very likely). So what else was happening at this time? The Republic was talking about creating an army (with the official opposition party being against it, though what the opposition was beyond The Naboo and Alderan is never stated), and the Confederate Droid Army made for their defense. And what was it that started the war, an attack on boarder worlds? An incursion into the Inner Core? An attack on the capital itself? No, it doesn't come from the Confederates at all. It's the Republic which starts the war, with an Incursion turned all out invasion of a Confederate world, which had been unprovoked as the only justification was the production of a fully justifiable army.
"But wait", you might say, "the Confederates started it with Jango Fett, who lead Obi-wan there". Well, the problem with that is, Fett was a private actor, which means he's the problem of whoever's territory he is in. When Obi-Wan was following him in his investigation, he was in Republic territory, in which he had the authority to do so, however, after he entered Confederate territory, his authority vanished because he was in another state, and was there illegally, so his actions where at best an illegal act and at worst the precursor to invasion.
4) The Confederacy was the underdog the whole time.
Now, when looking at the 'official' numbers of soldiers (which are wildly different depending on how one looks at them), one would think the Confederates have an advantage. After all, they have more droids right? However, the bulk of those droids where cheap worker units given a gun and sent into battle (the main battle droids where clearly created with cheap labor as their intent instead of combat, unlike the expensive Droidekas), and coupled with the manpower and economy the Republic had behind it compared to the Confederacy (up to 100 to 1 depending on the source), then it's clear that the best they could hope for was for their own independence to be secured. Just look at Coresant and the other Inner Worlds we are shown in Revenge of the Sith, they are not ones in a full wartime economy, they are clearly in a peacetime state with an active nightlife and a casual attitude towards even the war itself. "Oh, there's a war? I didn't notice. Wait, you can see the fighting in the sky? Well, the planetary barrier will stop everything. Might as well watch and enjoy the show". If the Republic was ever in serious danger of loosing, there would have been mass conscription and rationing of resources. Instead the bulk of the Grand Army of the Republic (another Civil War namedrop) is, for the most part, clones, as is the Navy, with the rest being local planetary security forces (which are glorified police, as we saw in Phantom Menace). Not that's all well and good, until you also realize...
5) The Republic uses slaves, and lots of them.
The clones are slaves. That's it. They where created to fight for the Republic, and no one cares what they have to say on the matter. They are shown that they have hopes, dreams, aspirations of their own. They give themselves names to replace the registration code that is used for identification, they give themselves unique haircuts to make it easier to tell who is who, they have different dialects which they use for casual talk, and it's likely that they have all manor of mannerism that are different from each other. They are sentient, self aware, intelligent beings who are indistinguishable from other humans within the Republic, and how does the Republic treat them? It forces them to fight against their will against an enemy they don't know for a cause they don't believe in. They don't want to fight? They never wanted to fight? Insubordination. Your rights? Sorry, not my problem. We never see a clone or two on leave, we never see them flirting with the local girls as real soldiers do, all we see is them fighting. And what happened when the war ended, did those who stopped wanting to fight get to? No, they kept doing their job as the army of the Empire. And when their creators tried to use them to rebel, then what? Then they took the most loyal, best of the best soldiers, and then committed an act of genocide against the remaining clones.
And so there you have it, the Republic man take many names from the Union's side of the Civil War, and many attitudes, however they where the evil ones, the ones using slaves. The ones who took the only hope that a large part of the galaxy had and smashed it to oblivion. And we are supposed to think of them as the good guys only because a few of their leading military where good people and a few of their opponents where less then honest.