I apologise if this has already been done, it is an idea. Would it be possible for there to be a first time build ability. What i mean is that the first time you build an Everest Class youi get an ability called Cole, with boosts attack for example. This way it could add more meaing to building capitol ships. Some examples:
Pheonix Class refit : Cutter (boosts defense)
Everest Class: Cole (boosts fleet stats)
Halycon class refit: Keyes (boosts individual ship performance agaisnt Covenant)