You are much better off designing your own ships. The core ships are never very good.Research the hull techs to get the larger hulls, and research the weapon and defense techs that can counter what the AI is using.It's a lot more fun to design your own, as well.
Plus, it takes a while for the core ships to adjust to shifted priorities.
I like that if I manually update a design, that all the planets building the old design switch to the new design, so I can get a similar effect while having better control over what my ships can do.