Well, I'm not a huge fan of artificial faction differentiation, I would rather leave those choices up to the player as to how he or she chooses to command his or her faction. If you want to play strictly canonical, the Empire pours its research into new starfighter classes (but not necessarily upgrades), while the Alliance heavily upgrades their starfighters. But you don't have to. If you don't want to use some units, then you simply don't build them.
While it does make their ships comparable on paper, the updated campaigns don't put the two factions on equal footing at all, so it's really a matter of being able to afford these ships for the Rebels. The problem is that a lot of people think the research takes too long or costs too much, and that's the only thing keeping the star destroyers and whatnot out of Alliance fleets. However, you will be able to pick a tech level in the next version, so you can choose how deep in the tree you start with ships unlocked.