I wholeheartedly agree with the idea. Perhaps making different types of ships would also be beneficial?
Currently the clearly differentiated ship types are Automated, Military/Militarized, Phase and Civilian ships. However, depending on their function, they could be categorized into different groups. Carriers, exploration vessels, combat-converted ships and logistics vessels all have different roles, and as such, should or should not a specific skill type. The Valkyre or Phantom have no right to take up military fleet points, while at the same time a buffalo with Militarized Subsystems has no right to count as a combat ship. I could imagine this working as build-in hullmods which give no bonuses other, than categorization for the ships. Or perhaps a new feature making it possible to assign ship types to combat roles (e. g. assigning the "Assault" tag to the Atlas Mk. II Superfreighter would make it a combat ship).
This would make it kinda necessary for the player to set ship tags and not just have a bazillion "Custom" ships. Not everyone would like it I guess. I find customizing my ships fun though. Anyway, that's my 2 cents on the matter.