Which is why you should ignore the module 'slots' and build a generic 'backbone' for each ship with the common required functions. For me, a suit change locker (removing the ability to suit change in a small SRV - perhaps in a larger one) and a bunk (respawn point if killed when not wanted) are probably the ideals.
Additional modules should be designed and fitted around the common cores. For some, they should probably be accessed by 'lift' (spawn mechanism).
.....
From a network point of view, this is why ships in Starwars Galaxies had opaque (from outside) windows. It culls immediately the need to network update on a frame by frame update the contents of separate ships TO the contents of separate ships.
A gloss black tinted outer window (for both concourses, buildings and ships) saves an absolute nightmare in network synchronisation.
Agree with both of these things... mostly.
As an explorer, I would (as I also keep saying) like the ability to spend time interacting with my ship.
Arrive in a system, stick it into SC, head toward some distant planet and then head over to the engine-room or an equipment room to tweak/service/repair things.
It'd be nice if everything
was physically represented as a "room" but it wouldn't be a deal-breaker.
Each ship could have, say, an "maintenance room" which'd be populated by doodads that represent all the stuff you have fitted to your ship so you wouldn't have to
see the actual thing, itself.
There could be stuff bolted to the walls to represent core-modules such as sensors, FSD, life-support, PDist etc and there could be a bunch of blanking-panels which get replaced by other doodads when you fit things like a shield, AFMU, limpet controllers, SCBs etc.
Basically, a ship interior
could consist of just a bridge/cockpit, a maintenance-room, an engine room (optional) and personal quarters.
The only other "cheat" required would be related to SLF/SRV hangars.
They would need to
seem to be in a plausible position, near the bottom of the ship - which'd mean setting the game up so that whatever size hangar you fitted, and however many hangars you fitted, they'd always appear to be in a plausible position.
I might be wrong but it seems like that
should be easy enough to achieve simply by accessing them via an elevator, which always takes you to the desired location with no regard for whether those slots are, physically, where they "should" be within the ship's interior.
Obviously, this wouldn't be acceptable for those who want to be able to wander around their Annies/Belugas/Cutters and look inside every cabin or inspect all their cargo but it'd be fine with me.
