1) The more time a server last, u will see more Dreads and chesse ships out there. In order to avoid the cheese fest, make the Capitol and Special ships more expensive in Building Points terms. If u have a 2 weeks servers, then use a determinate price list; if is a 3 weeks server, use another more expensive.
2) Other way to make the Capitol and special ships more hard to build is stick more to time and pilot skills. Let say, if a fly a F-CB for X amount to time without getting kill, and if my empire have the X amount of Building points, then I can upgrade my ship to Heavy Battle cruiser. This idea have to 2 mayor issues : One is that the pilot will be more careful and he will tend to run in a P v P situation, and Two is the casual player is going to have a more difficult time in order to fly a C or S ship. To avoid that, we can use rules who cause losing VC points for disenganche; for the casual player, we can use Dizzy Lotery idea.