I will just use general references, to save time:
Pirate Flagship
Ship Abilities
Special Crew and First Mate
Here is the leading design so far:
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Every ship will get a list of new abilities.
-These abilities will be like the current upgrades (these will be regarded as basic abilities that EVERY ship has)
-Different ship types will have different set of extra abilities
-Just like current upgrades, abilities will be upgradeable with attribute points.
New concept: Crew Experience
-Crew Experience will increase the maximum attainable level of a ship.
-Crew experience will be gained from battles for War Type ships and from Trade Routes for Trade ships.
-Crew experience will be intensively hard to get.
-Crew experience will be irrelevant to crew number.
Ship leveling details
-Current max of 10 levels will be retained as basic max - regardless of crew experience.
-Initial max limit will be set to 20 level (This means 10 different levels of crew experience).
-Every level upgrade will use current system in attributes (3 to 5 attribute points per level up)
-We might use a different pricing module for levels beyond 10 as some ship prices will get really high if current system is used.
-There will be a limit for ability upgrades beyond level 10; they can't be higher than the ship level (so a level 14 sloop can have at most Cotton sails of 14)