I start with a technological theme for each organization, giving me common shapes and colors, then look at function and how that affects design. If your carriers look like your destroyers, you are not putting enough thought into the function. A great example is Star Trek II The Wrath of Khan. The Enterprise and the Reliant are clearly designed by the same military, but one is a heavy cruiser designed to explore distant starsand the other was a light cruiser meant to stay closer to home. From stem to stern your ship should have function in mind. A carrier will be dominated by launch bays. A cargo ship by its cargo area, a battleship is a mobile gun platform, a suveyship is designed around sensors. And its okay for some significant similarity between a cruiser and a destroyer. They do similar things. Look at a navy frigate and a navy cruiser. You have to be really knowlegeable on ships to tell them apart.