Unique ships, those that are exclusive to only a handful of people tend to bring out a lot of jealousy and I think its fair to say a touch of elitism amongst those who wield such ships. Having one or two ships like that can make for interesting encounters for a short time until eventually folks get bored and those ships end up in mothballs, locked away from anyone who would try to restart that character or worse yet, try something different with it.
Each of those ships are connected with the character they were designed for, perhaps not in lore but by those who remember interacting with them and as such are inseparable. You couldn't see the Necrosis as the Outcast's flagship, it's reputation as a madman's weapon of destruction wouldn't allow it.
That brings us to the point of the matter, unique ships are good for a time but are extremely limited. However rare ships are an entirely different kettle of fish. Take a look at the Barge, it's just as noticable as the unique ships but it has none of their limitations. People RP it as a base, a mobile factory, a supertransport and even an entire company. If any ships are to be added, let's make them adaptable and useful, not museum pieces locked away by sentiment.
After all it's the character who defines the RP, not the ship.