I was thinking about this tonight because it's 4 a.m., I can't sleep, and I think I have a chemical imbalance.
Anyway, So we see the political climate in Episode One right? It's a half-@$$ed democracy of sorts, where not only do individual planets have representation but also financial institutions, and Business organizations... It's also likely that trade guilds and labor organizations have some say in the galactic political process as well.
At the same time, it's this obviously corrupt and very slow process that leads to a civil war.
The "Separatists", or Confederacy join together to form an independant government aside from the Republic. The Republic doesn't want this... The most "recent" event we can liken this to on Earth (That the majority of us reading/contributing to this topic can relate to anyway) is the U.S. Civil War... The Confederate States of America seceeded from the United States of America over individual rights.
It's similar in a way...
Now, we're led to believe the leaders of the Separatists are inheritly evil by Episode Two. I don't necessarily BELIEVE they're all bad (Though I think it's established the Neimodians are). EU has established several planets joining the secession as well who are leaving because they're genuinely fed up with the crap government handed them by the Republic.
OK, so by this we see that regime change was needed, right? I mean, WE know the Republic was crap...
Problems could abound in the Republic's world that we have no clue of... We know the Naboo conflict was one issue, and thinking of it in Earth terms it's as if the whole of our world's population were overthrown by an invading force, with millions of casualties... That's a mass issue. That's the equivalent of World War 2 happening within a month or so, for an example.
That's ONE conflict out of who knows how many other civil wars, conflicts and other issues that can be directly blamed upon the Republic's very poor structure.
OK, so the "dark times" come... The Clone Wars end, and the Empire takes over... The Empire gives some "System's rights" up until the events of A New Hope we know, because it's not until the Death Star's completion that the Emperor dissolves the Senate.
The Empire brings with it a change of rules I guess... In some EU writing, the Empire's got some "fine points" set out that you cannot possibly get from movies that show it as 100% evil. For instance the Empire sets up control on trade so that groups like the Trade Fed. cannot pull their blockade BS. The Empire restricts arms trading, and expands space exploration/colonization. The Empire takes a personal interest in every colonized world, either through small patrols or full garrisons. The Empire attempts to curtail the "Scum" of the galaxy like Han Solo. The Empire establishes training and schools. In the game TIE Fighter, the Sepan Civil War (A system of human inhabited planets) is ceased by Imperial Intervention that's fair and just for both sides.
Anyway, we all know the "bad" stuff that comes with Imperial control as well... The slavery, Alien prejudice & human priority, martial control of the galaxy, mass propoganda, control of personal freedoms, etc...
Now, during the Empire's time, the another civil war breaks out... Several planets ally with each other, much like the separatists did prior to the Clone Wars onset. They title themselves "The Alliance to Restore the Republic". Sounds better I guess. The Alliance seems hunky dorry by the film's view, but what are they asking for?
Well if they're truly wishing to restore the Republic, are they wishing to restore it to how it was? It was pretty darn crappy by my estimation... So why would you WANT to restore it? Would crime run rampant again? Would political backstabbing the wheeling/deeling of politicians not take over once more?
What's so great about the Alliance other than they say the Emperor's a bad guy, and point out where he is bad?
OK, so here's my question... Which government do you want? I'm going to request that you THINK of this as a human... IE: Don't think "Well man I like wookies, and so I'd hate to be one in the Empire's reign"... Just think of it like you're a human, though having some sympathy is fine if that's what makes you choose the choice you do.
Alright, this is a goofy topic, I'm sorry... Maybe it's just me, and stuff like this keeps my interest.

Feel free to ignore the topic all together if you find this 100% boring.
I'm thinking that I'm actually leaning towards the Empire... I'm disheartened with the Republic after seeing the prequals. The Empire sort of brings a "hope" the Republic didn't. The only thing is, the Alliance is thinking idealisticly, and maybe they'd planned government changes to curtail political wrong-doings that ran rampant in the Old Republic. I dunno...
I'm a bit on the fence on the issue I guess. If you've played TIE Fighter, you'd be on the fence too. It's quite an interesting story, and after playing it (And reading some of the "Empire's Side" in various forms) you'd question this too I believe.