Arming and sustaining Atlantis as a capital ship

How should Atlantis be armed and supported if a city ship is expected to fight as a capital ship?

Add layered gun defences, internal hangars, and automated production for Puddle Jumpers and defence satellites instead of relying almost entirely on drone weapons.

The fictional Atlantis city ship relies heavily on drone weapons, but a vessel of that scale would benefit from large guns and layered defences as well. Its size should also support automated facilities able to replace defence satellites and Puddle Jumpers from stored patterns. Bringing shuttle bays inside the hull would protect small craft and their support spaces. A later exchange accepts that the Ancients may have intended city ships as protected, lightly armed habitats, while pointing out that Atlantis is repeatedly used as a capital ship and is too valuable to remain lightly armed. Onboard production and protected aviation spaces would let the city ship recover from combat losses instead of treating each destroyed small craft as permanent.