After starting the new game, I immediately opened the shipyard associated with my home world.  As shown in the first screen snapshot, there are a number of ships available to build that should not be there.  Each of the "extra" ships that I can build is based on a specialty ship (Prospector, Raptor, etc.).  In a previous game, I created modified versions of the specialty ships and those modified ships are now immediately available for me to build.  This raises a number of issues:

1. Why do you allow specialty ships to be modified?  This allows players to create multiple copies of what are supposed to be unique ships.
2. Why do these modified versions of the specialty ships show up as available to build at the beginning of the game?  As shown in the second screen snapshot below, the ship design named "Ysengard 17.1" has 2 Graviton Guns, Barrier Fields, and Carbon Crystal Plating, none of which has yet been researched (obviously!).  The only factor limiting which of the modified versions of the specialty ships that I created in previous games is "Mass".  As I research technologies that allow higher mass limits, additional modified specialty ship designs will appear.

I suggest that players not be able to create modified versions of specialty ships.  If you decide that you still want to allow modifications to be made, then I suggest that the available ship designs be filtered to require the features that are included in the designs to have been already researched.  The ability to build advanced ships early in the game gives me a tremendous advantage.