Ship proposal:
1 x Bridge
2 x Dorms
1 x Bio Lab
1 x Tech Lab
1 x Archaeology lab
2 x Reactor
2 x Engines
1 x Space FTL Drive
4 x Hydroponics bay
1 x Shuttle bay
1 x backup reactor
1 x AI core
1 x Medical bay
1 x Brig cell
1 x Isolation chamber
1 x Smeltery
1 x Manufactory
UNDECIDED x weapons
UNDECIDED x shuttle craft
I recommend a second FTL, that thing is irreplaceable. Gotta have a redundancy. Don't need to power it ever. Also I suggest several storagebanks for computers, since the ship will have a considerably smoother function when the ship gets larger if the AI can make a few sub AI to control additional modules and have room to code another primary AI for any ships we build/acquire.
I recommend two or three isolation chambers, personally I would rather have a chamber for every crewmember, but that's not logistically reasonable.
Maybe a secondary brig cell. So we can store leeets say a mutinous crewmember and a hostile alien without the crew member being eaten.
At least two shuttles. Probably several load carrying drones, combat drones, and mining drones.
Weaponry, since the AI will be combat grade and capable of handling several at once, probably should have two or so particle beams for mid to longrange. Maybe a pair of missile launchers, can build missiles onboard. Salvage laser for salvaging. Drones can take care of mining. Maybe a railgun also. And four Point Defense turrets.
2 primary engines are fine, would prefer three though so we can turn even if maneuvering thrusters are dead., but we need maneuvering thrusters. on the sides, front, bottom, and top.
Two backup reactors, four online reactors.
Bulkheads throughout ship to rapidly seal hullbreaches.
Second biolab so risk of cross contamination is lessened. Also need a way to completely seal the biolabs so no pathogen outbreaks occur.
Personally I would prefer a second bridge for redundancy, even though the AI can control the ship and will likely handle most flight and combat, in the event that the ship is so heavily damaged that the AI is offlined, the primary bridge likely will be destroyed.
Personally I think a second Hydroponics Bay would be a good redundancy, but not really necessary.
Need a Refinery. Preferably two.
Need like four or five cargobays.
Preferably secondary Smeltery and Manufactory.
Preferably an extra dorm just in case we recruit anyone or if one of them is destroyed in combat.
Secondary tech lab would be nice. Also should have its own storage banks.
We should have a number of redundant storage banks.
Archaeology lab should have the same sealing system as biolab. And probably a second one would be smart.
Atmospherics module for rapidly pumping or removing air from and to areas of the ship, useful for fire control, also useful for if we have an alien that can't breath standard oxygen, we can pump a room with their gas.
Various drones can just parasite off the main ship.
We need a launchbay for new drones though. Probably a Drone Manufactory specialized for drones built into it so we can build and launch mining equipment on demand rapidly. As well as retrieve air volatile samples and pathogenic materials.
Most drones after construction can just parasite off the hull. Just latch on and stay put.
Ship should probably rotate so some parts of it have gravity.
Should have fairly massive cooling fins.
A light shield is mandatory so people don't get fried by solar flares or get cancer from radiation. Doesn't need to be strong enough to stop physical objects. Would be preferable if it was.