I can't believe I'm going to post this, but here we go.
In many cases, I think Carrabean: Blood & Gold has a better structure.
1) Balance the economy. You can actually make too much money too quick here.
2) Get rid of the basic/common/fine/exceptional.
>Each boat has an initial cost. If you can buy it, you can sail it.
>If you can cap it, you can sail it, but sailors cost money (not as much as they do now) and you get only a set amount of freebies no matter the level (for argument sake, say 40)
>Available upgrade slots are limited by ship size. Cutters and lynx get 1 max, while SOL can have 5.
>>Upgrades cost money, or can be unlocked from loot. They attach to current ship and cannot me moved to another ship.
> Ammunition cost money. You ships will have a limited ammunition based on you current ship, and if you use it all up, your need to go to port and buy more.
> Ship can hold less repair kits.
Then what about levels?
Your leveling will be more like you officer. You will get points as you level to put into skills that can improve certain ship type function, or if your skill is too low in that type of ship, you suffer penalties. The ship types would be (Traders, Light, Frigate and SOL). On a ship, you might see frigate level 3 on it, so if you are frigate level 1 or 2 and man that boat, you suffer a (10% * level difference) penalty to steering, reloading, accuracy, speed. If you are above it, then you get a (5% * level difference) bonus. Maybe have each class have their own experience paths so if you're In a frigate, you get frigate experience.
The current ship rating, as you poorly word it in game, is mostly meaningless, and can be confusiong when it comes to the officer traits.