Having done some IVA in the current version of RS I know that you replace stuff like batteries and air filters (when they are full).

But stuff like this:
https://youtu.be/I270vSrTIuk?t=7m40s

.... I feel is needed in RS.

The ship systems and constituent components should be broken down into interactable elements onboard the vessel.
It should be possible to:
* Repair (lightly) damaged components.
* Reset failsafe mechanisms.
* Replace FUBAR components.
* Upgrade with better versions.
* Sabotage (replace with component that will fail/explode on timer/remote) or doubling as a tracker/beacon/transponder.
* Reap tangible benefits from having additional crew. A good chief should somehow yield some additional ooomf from elect subsystems.

It would expand on the existing gameplay.
It would provide tangible benefits from being more people in the same vessel.
Given a few choices both in ships/system/subsystem/components/subcomponents, the opportunity to customize your ship would be exponential.

Research levels, stolen tech, discovered artifacts, phenomena/encounters could all contribute to options in the ship customization.