Technically.. neither army is better.
But if you just compare it on Paper Versus Paper stats, empire will, and should, completely Steamroll the Rebel alliance each time, if we use Only Paper Versus Paper stats.
I'm almost, or was, an Exclusively Rebel player. There units are majorly inferior to most of the Empire units. Nuff said. Their units will Not win against Empire, capital ships/frigates/cruisers I'm talking about here, in a 1 versus 1 brawl. Tried and tested it many times, Empire just has more firepower.
However, Empire are not mobile, at all. They are not as fancy as the Rebels and they can't afford to do some of the innovated maneuvers a skilled Rebel player can do with ease.
I've always ran into the argument that Empire is superior in space. For a long time, I thought that to be true too. However, Rebels are just as good. I'm not going to say on-par because in all honesty, they are Not. A Rebel fleet going toe2toe with an imperial fleet of the same caliber of size without micromanagement Will get decimated. Rebels require an all together different game-play method. In campaign, the Empire sure as hell can afford to Throw units at their enemies repeatedly because they have one heck of a stable economy during the early games. Rebels - if you do that, you die. Simply put. Have to adopt Guerilla warfare tactics but I digress.
Rebellion Alliance > Empire