Well, like I said, the setting works with relatively widespread A.I.s, so you could make a ship without human intelligences entirely. I usually just rebuff that by pointing out that a lone A.I. on a ship could go mad, and would be significantly more lethal than is tenable. Human crews (outside of colonization which obviously requires humans) are more a safety net to overwatch the A.I. system in the ship - the A.I. controls weapons bays, conventional thrust, and a bunch of other stuff, but is explicitly locked out of systems that would kill the crew before a response could be formed. A.I. in this setting are also hard-locked into semi-portable spheres for similar reasons, so there's something to destroy that gives the A.I. a physical body.
Warp-speed missiles are just too expensive to be worth it, particularly since installing an A.I. on one is liable to A) piss other A.I. off (they're people too, with rights), and B) would make it even more expensive. And an A.I. is pretty key for ECM warfare, since they can make snap decisions with creativity at speeds a human couldn't compete with.
Returning vaguely to topic, this setting also has a system that I wish they had used for Stellaris. I would have much preferred breaking travel into two distinct engines: The warp engine, which a ship could use to jump to any system, but very, very slowly, and Warpgates, which would function like roads and allow for quick travel to explored systems. Construction ships would have to build a gate at the starting system, and one in the destination system. Afterwards they would function much like the hyperlanes we have now.
I just want there to be a macro-scale infrastructure aspect to the game. Hyperlanes already being there makes neat galactic geography, sure, but it removes any reason for civilian ships being in your territory beyond just idle shuffling about. You've already built all your mining stations, so there's nothing much left for them to do until you decide to finally build that dyson sphere.