imo it will be quite difficult to have truly personalized ships.
historically the different nations had different designs for the same class of ships. and those designs improved over the years.
for ship specialization i suggest that each port gets a small unique flavor for a ship. say an lmm build in psaral is slightly faster than a regis built lmm. a brig from tortuga has holds more cargo etc. (good for large nations since dukes want multiple ports to built ships
)
for general ship type improvement i suggest that ships get randomly a buff each time the ship ID# counter passes a multiple of 5000 or 10000.
the random buffs could be increases speed, more HP, larger cargo space etc)
it will change the game for newer ships will become more powerful than the old ones, which is realistic. it will devalue old ships on the auction which is good for new players. also it will boost the economy because the new models are better thus give you the edge you need to stay ahead. (my parrot whispers that some of these newer options are going to require 1 or 2 goldbars to guild the captains cabin