I'm going to repeat something that's been said a few times, primarily by the esteemed master o' mod FoshJedi. A giant counter ship simply is NOT the Rebel style. The Alliance To Restore The Republic was about subterfuge, speed, fighter strength. Their Mon Calamari Cruisers were very rare in the Rebellion fleet. Later on, as the Rebel Alliance transforms into the New Republic and then in the wake of the Yuuzhan Vong war into the Galactic Alliance (btw, if we ever see a Yuuzhan Vong game, I will literally bawl tears composed of pure happy joy), we start seeing some of the bigger ships, like the MC-80b Mon Remonda class, the MC-90 Defiance class, the Viscount and Strident classes of Star Defender. Now that it's a legit government, it has both the resources and legitimacy as a government to field massive battlecruisers. However, the expansion takes place in the Death Star II, Later Stages of Rebellion era, and the Alliance just didn't have a huge cruiser fleet at that time.
The point has been raised, and I again raise it, that the Executor and Eclipse classes, while being very intimidating and impressive, does NOT imbalance the game. B-Wings, Y-Wings, those alone with support from X-Wings, A-Wings, and Corellian vessels for TIE defense, can lay low one of the big ships. Like another guy said about the pop cap, if he has four ISDs and one gets taken out with an ion, and those ships took up all his popcap points, the Rebels CAN take those ships down.
Like the dev said, though, in the very end, gameplay over realism, always.