Now with that you could have an opportunity to have a 'shore leave' episode mission or have to fly around in a lower tier starship until Fleet Yard notifies you that work on your ship is complete. Of course this idea will most likely be unpopular, but I intend it with an eye to add that little bit more realism to the game, and of course as I said it would allow for some sort of Genesis inspired shore leave event where you get to visit some locale for a mission, be it Risa, Earth, Vulcan or maybe somehow link it so that you have your mission on your characters racial homeworld.
While at lunch I had another consideration for a background mechanic that might add in some more interesting possibilities. Consider this, you have just had a stint in drydock and refit your ship, be it with new engines, warp core, ODN network, whatever. On your way out of Stardock and somewhere in sector space, there is a chance, and by chance I am thinking minimal but still possible, that you have a 'failure' of some ship system, stopping you in space. Now this could branch depending on circumstance so that you have to repair the ship system, or possibly repel boarders taking advantage of your ship being dead in the water. This will of course play into the new interiors that we will have access to. Just a thought.
Not really fit for this thread, but yeah something like that could flesh out the random encounter in sector space a bit. Expand on the constant defend sectorspace encounters with other random stuff like the above or distress calls, etc.