I understand the frustration when the Captain leaves the crew the rest of the crew has no longer the possibility of gaining process in the milestones.
But I think adding this kind of feature would lead also to switching ships just because someone needs some milestones; if so, Rare should remove the ship milestones, as they'll be no longer any resemblance of what a ship and her crew did.
I like the fact that you can spot the same ship you encountered earlier over a longer distance and don't have to rely on your memory of their sails for instance. I (or we) still play this game on the server we start with (unless some very unfriendly situation happens) and kinda try to read the other crews.
Oh, it's the Brig Lebowski, they were friendly earlier, lets not disturb their Veil fort; or, those just kicked our buts, keep clear; or, I guess they're still on a Tall Tale, &c.
When ships can change their identity on every whim, this recognition will disappear and captaincy will just be a set of meaningless milestones and an ever changing name on the crest.