The Rebel Alliance is a difficult faction to play. Generally we have found that late game the Rebels can be among the most powerful factions in the game. But it is hard to get there, and that is somewhat on purpose, as we want to make the Rebels feel like the underdogs. As you can imagine, its not an easy task to make a faction feel underpowered while actually being balanced.
That said, the next update on Monday will have some major changes to the Rebel early game, along with a more traditional New Republic faction if still don't like them but want to play a good guy faction.