Okay, listen, I love the Rebellion. I actually thought most favored the Rebels, but I was wrong. And I am not following a fad, I hate fads. But here are my comparisons(based on stats, not on which I favor):
Most people thing Mantas stink, but when I play the Manta wins 95% of the time that I see 'em battle.
Every major battle that I see between Rebels and 'Feds, the Rebels win.
Torpedoes are slow but have lots of damage, i'll give you that, and i do prefer them to missiles, but missiles are faster. And they have more than enough damage to get you through. They also fire easier if you have a ship that allows you to fire several missiles/torpedoes at a time.
I think all the Rebel ships are stonger, based on experience of the two battling before. I even thought this when I was considering thinking that the Confeds were better.
A fond nickname I have for the Confederate Frigates: Confederate Refrigerators. I dunno, those two words sound alike to me. And the rebel Destroyer has a teasing name because it's only fair, but not as good: The Rebel Employer.
There ya go. Also, the cloaking device is really cool and comes in handy when you're in a very violent system (like somewhere three times as bad as Darven, you could say, or when you're fighting the surviving aliens.)
I have never become an official Rebel, because at the point when I got to fighting the aliens, you know what I had? A Scoutship. Isn't that funny? Pathetic, but funny. I didn't get a Corvette because I'd be damned broke, and I didn't get anything else because 2M is, to me, hard to earn because i hate missions that are too far away. That's a downside for the Rebellion, because their government sytems are surrounding the Core Worlds.
A good thing for the Rebellion: The HQ of the Rebellion is placed near other Rebel systems. The Confederation HQ is plunked in the middle of Rebel systems. It might be a little less predictable, but once they find out, which the Rebels have, you're pretty much sunk.
And anyone who likes the Confederation more and is sexist, don't use the fact that I am female for my reasoning to be sh*t. 'Kay? 'Cos I ain't helpless.
In short, it's the Rebellion all the way.