Hm, just experienced something similar and started a thread about in "general" (yeah, should have looked here first), I did not save my ships as templates though, but just as normal ship, but without any weapons etc yet (for further work later).
Hope this gets changed so that these ships become accessible without starting over. I also would love to have the ship designer working from the main game menu, like in GC II, where you just could create a bunch of ships of any size, then launch a game and have them available there once the techs needed are researched.
