No doubt this will be another area that will undergo some change.
I'm hoping that they retain the cosmetic freedom of the design system, but implement a more deeper design system for ships. GalCiv 2 ship design is just cosmetic freedom, nothing more. It doesn't matter where you put your engines, your weapons or any of your modules on your ship, none of that matters.
I would really love to see a sort of Star Drive ship design mechanic, or something similar in that regard so that designing a ship will involve a bit more strategy.