If Mr. Stahl doesn't even want to charge a higher rate for slots past this limit (to offset the laughable storage cost) then its time to give up as they will never fix this for you. Some devs don't even know it exists.
...is turn the reclaim option they have when you turn in your c-store ship into a shipyard. Goto the shipyard and instead of it being called "Reclaim" it would be called "Acquire" or "Get" or "Use" or something on that line. I am sure there is a better STO way of saying it but it is that simple. The capabilities are there and being used already all the servers have to do is save as a text file what ship that person has and then create it when they ask for it. I don't think it is any different than it is now, you just have a picture of the ship.