Certainly some ships are intended to replace others - that's one of the benefits to researching - but I'm using the upgrades to make them more unique. A lot of them start out quite similar because canon dictates such, but think of it as the last common ancestor of an evolutionary divergence. The Dreadnaught/Dodonna upgrades are one of the better examples of this. They're basically the same ship to start with, give or take a few cannons and some cosmetic changes, but the Dreadnaught accepts its speed limitations and opts for better armor and more weapons, while the Dodonna essentially becomes a 700-meter frigate in terms of speed and maneuverability.
But, uh, yeah... Imperial raids and Rebel hangars are staying. It's just way too much of an artificial way to differentiate the factions and comes across as forced.