Here are some suggestions.
General ship desing suggestions: Directly connectable rooms: From the videos I have understood that different rooms can only be attached to each other with doors. If rooms could be connected directly to each other it would have several benefits: you could for example just directly attach power relay to power generator room. This would save some precious money, space and energy a door would demand and it would make the maintainance more efficient (shorter trip between rooms and no door that you would have to breach trough if the relay was down or invaded by enemy), maybe a little maintainance boost could be added like "10% quicker maintainance for each room" because they share the life support systems, power cables are easier to access etc. Downsides of directly connecting rooms would be their increased exposure to risks like fires, hull breachess or enemy infiltration. Rooms could also be connectable with open corridors, this would be a compromise bethween saving some money and energy and slightly limiting the spreading of fire and movement of enemy teams.
More different sized and shaped rooms: These are propably already planned but here are my suggestions anyway. In the video I only saw one type of cargo units for example. I think this really limits the number of different working layouts for the ships (in that tutorial the forward section of the ship was pretty much the only place where the cargo unit would fit without pressing some vital systems to too dangerous places and/or not providing protections for them. for example I would like to build wide cargo units with side access points to the sides of the ship so that vital systems would be better protected from the sides, or maybe build smaller bays all around the ship to give general protections and to not lose all the cargo to one asteroid. This goes for pretty much all rooms in the game. Different sizes and shapes would not only give countless new sensible layout possibilities, but also increase the number of "economy vs safety" options: build one huge fuel/air/water tank and risk losing it in one blow, or build several small ones all over the ship to increase safety (but also price and need for maintainance).
Room suggestions: Fortifield corridors: These would be corridors that have been designed to be easily defensible to one direction (bunker style structure at the other end and nasty stuff like barbed wire at the other). These could be used to protect vital areas of ship or prevent enemies from spreading out of the easy-to-infiltrate areas. Dowsides would be the increased cost of these corridors, and the possibility that enemy comes from the unexpected direction and uses the fortifications agains defenders.
Automated defence corridors: These would be corridors with automated defence turrets. They would be expensive and energy consuming, but also really efficient way to defend the ship. Real risk would be that the turrets are controlled by the AI core, so if enemy infiltrates the core (or AI goes rogue) the guns would be turned on the defenders.
Blast Doors: More resilient version of the normal doors, these would have increased price and energy consumption. Also if power relay is knocked out these doors would go to lockdown (if power relay is knocked out normal doors would become manually operatable, which is faster for enemy that breaching, and slower for friendly forces that just walking trough them) so do you block the access to your fuel storage with light door that can be rather easily passed trough by everyone if relay is down (risking enemy sabotage), or do you rather build heavy door that locks down without relay, and risk having to breach trough it yourself if theres fire that needs extinguishing.
Internal sensors room: This room will show you what happens in the rooms where there are no friendly crewmembers. If the sensor room is knocked out you won't see what happens in rooms without personnel, you won't see enemy movement of notice spreading fires, making it tasty targer for those enemy infiltration teams.
Command bridge variants and specialized-bridge-modules: Different sized bridges that need different numbers of pilots (and energy) to operate and effectively command ships of different sizes (for example: small bridge need 3 pilot for example and can effectively command 15 man crew, large bridge with 15 pilots that can command crew of 100) Too small bridge would decrease the morale and general efficiensy on the ship. The specialized bridge modules would be bridge extensions that are attached directly to the bridge. (examples. Tactical room: operated by three marines, increases the max crew size by 15 and gives all marines morale and efficiensy bonus. Weapon control room: operated by three pilots, improves the accuracy and reloading times of ship guns. Damage control room: operated by three engineers, increases the max crew size by 10 and increases the morale and performance of the engineers while repairing or maintaining ship.)
Heavy Armory: instead of arming the marines with basic suits and rifles it would arm them with combat exosceletons and heavier weapons. These armories would be much more expensive, energy hungry and demand a larger room and naturally make the fighting forve much more efficient, but also smaller and therefore more vulnerable. Together with brige options this would open up a ton of different desing philosophies for the ships: Combat ship could be a huge carrier with dozens of marines for cannon fodder, or a small high quality privateer craft with small bridge and tactical extension, housing a team of space hulk style killing machines (maybe the exos could even be launched directly to enemy ship in some kind of small landing pods instead of having to have the large hangar bay, further making it a small size option).Or maybe a medium ship with couple squads of marines and few heavy marines to support them.
Water and Air prosessing plants: These rooms would decrease the comsumption of water or air. Large crew ship would demand a lot of water or air tanks, so option to save some space for more important stuff by using water and air recycling plants would be welcome (example: you ship can go for 3 months with 4 air tanks it has, air recycling plant will recycle 75% of the used air so with it, the 4 tanks would be enough for 12 months, or you could remove three of the tanks and replace them with cargo unit and still go for 3 months) These recycling systems shoud be quite small but expensive and very power hungry (espesially the air one).
Weapon suggestions I have seen lot of great weapon suggestions on the forums so I'm only going to put here the ones I don't think have been suggested
Flak guns: These fast and accurate, small caliber weapons would be almost purely for anti-boarding-craft action. For lightly armed cargo ship a convetional anti-ship guns would be almost useless making it only possible to fight other lightly armed cargo ships that won't be attacking you anyway. Largest risk for these ships are enemy boarding parties trying to steal your ship and cargo intact. For small cargo ship with small marine force a flak gun would be an ideal option to delay or weaken the enemy attack so that heavier ships would have more time to come to rescue.
Anti-ship-turrets: Not sure if the game can support this, these guns should be destroyable even if there still is rooms around them. These turrets would be genarally placed on the highes or lowes decks so the actual gun part would stick out of the ships top or belly (or mid decks in places where there isn't rooms on them, pretty much the opposite of lift/stair placemet system) These turrets would have larger firing arc than the side turret but they would be more expensive and power consuming.
These suggestions would in my opinion add a lot of different options with up and down sides to the ship designing, hopefully helping to slow down the ship designs from going towards few optimized designs that can't be beaten with anything.
PS. This project looks really promising
I have been waiting for a game like this for years. Hopefully it will go far. Good luck!