I suspect this is one of those "easy to suggest, hard to implement" things.... but here goes anyway.
Examples:
- Reverse docking: http://starmadedock.net/threads/reverse-docking-beams.7086/
- Can we have a method (special rail docker, or rail, or whatever) that allows the primary ship to integrate the systems of docked structures?
- Bonus: Might we even engage or disengage those systems depending on the rail position, or change the rail position based on the function of the structure?
- "t" menu systems from the docked structure would appear on the "t" menu of the main ship.
- Thrust and power from both structures would be calculated as one.
Examples:
- Star trek: Intrepid class: The warp nacelles rotate into position before warp-jumps. Yes, we can simulate the effect, but it feels silly having purely decorative warp nacelles when all the systems are in the main body of the ship, or getting my nacelles blasted off, but still being able to warp out.
- Star Trek: Klingon B'rel, Star Wars X-wing & B-wing: All these ships have primary weapons on the ends of movable appendages.
- Firefly: Firefly class: Vectored thrusters that pivot on the ends of structural booms.
- Star-wars: Jedi fighters which reverse-dock to their FTL jump rings.
- Star Trek: Galaxy, Prometheus and several others. Compound ships really only make sense if the systems of the docked ship become an integrated whole. Imagine a Galaxy class ship as two parts. As soon as I docked, half my ship would become inert dead-weight no matter which half I decided to steer from.
- A tug boat might reverse-dock to a larger craft, temporarily becoming the pilot-house for the craft.
- A smaller cargo-handler, might reverse-dock to a cargo pod to move it from one ship to another