Ok, the problem is simple, 95% of player crafted ship are exceptional, the simple reason being a Exceptional ship is exponentially better than a basic ship and the cost in labour and resources between a basic and exceptional is minimal. Players can easily acquire the money and resources to build and purchase Exceptional ships so that is what is used almost exclusively. There are 4 quality levels which are not utilised and I believe should be.
There are numerous solutions to this problem but in essence I suggest each quality level of ship should be exponentially more expensive in both labour and resources. Keep basic ships how they are, materials and labour are good, they require some work but every player can afford ships but not so much that they are disposable. But lets for instance sake make each level of quality require 5 times more resources and labour (Call it the shipbuilder selecting the best materials) so that they really are special. I'd be happy to see exceptional ships cost 50 times the materials and labour they currently do, sure not many people would use them but that's the point! People will still build them and they will be expensive as hell but they will actually be "exceptional" ships not just what everyone sails.
It will have no effect on people being able to play and enjoy the game, basic ships will cost no more than they currently do BUT people will start using them! Those small bonus that higher quality ships give will actually mean something in pvp because not everyone will use them!
There are a few different methods that could be used for increasing the labour and material requirements for higher quality ships, the method is irrelevant, crafting notes, potbs "lineship bundles or MOV's", use of rare resources or simple huge increase in common materials but lets make higher quality ships expensive, really expensive and special not common.