Could be fun to build custom ships kinda like the gummi ship builder in kingdom hearts.
I'd imagine it would be a simple scrap based buy system, with easy/normal/hard giving less scrap to build the ship as it gets harder.
To get the ball rolling I'd suggest normalizing weapon costs for this section as well as missile/drone costs.
Aside from the base requirements of a ship being power/sensors/doors/O2, additional rooms could cost by their size, a simple grid based GUI could make the building process simple, and it opens up a world of builds, augments could simply be unavailable or very expensive at this time. Crew could be an increasing cost so getting a large crew would be difficult.
All and all despite making the game easier for some I'd love it as a future addition.