I agree with your perspective here almost in its totality, but I do think there is one problem in terms of design space.
The droid upgrade.
Sure, the imperials have the bomb upgrade as unique to them, but it has a single function use. The droid slot allows for a lot more flexibility and tend to be cheaper for what they do. You can improve maneuver, shields, make your ship more agile, and on upcoming droids add stress to an opponent or even add an EPT to a pilot that doesn't have one.
There really isn't anything on an imperial ship that is going to make up for this kind of flexibility. Maybe they need to add a "Dark Side" upgrade or something to certain ships, I don't know, but the droid is providing them with some design flexibility on some of the rebellion ships that just doesn't exist on the Empire.
Maybe it's time for some Imperial Only modification cards to set this whole astromech inequality to rest...