You know there are old games which are still well remembered because of their unique concept. Like Master of Orion where you could customize a whole ship by filling the ship outlines with system, weapons, shield, generator and even armour plating on your own. Another game like Stardrive also apply a similar system. So you could build the ship just like you build any house on the planet but only within the ship outline. The outline for ships could be researched to discover them (scout, frigates, battleship) along with it's weapons and other systems like sensors, generators, hull plating and shield. Combat could be done by sidescroll and the ship becomes an entity or player character itself with the stuff you build into it becomes it's equipment (Stardrive ship construction system offers the best solution for it to be applied in Starbound). Also combat could be done turn based but energy allocation for system and crew members manning the stations like FTL. Not sure what people complaining about "originality", some of star trek game used this concept in the past only FTL used it best. Well it's up to the game maker to decide on the licensing issue... And after space battle you could go on spacewalk to "mine" and "salvage" stuff from defeated enemy ships (rare ores only available from shipwreck perhaps?). In addition if you place a cloaking tech option you could sneak into enemy capital ship/station and defeat them from inside...hmm, like Star Wars maybe? Take out the control room/boss and you defeat the ship? Although you should make the ship defenders and traps so horrible that it will be an extremely difficult but rewarding experience. You could place physics function like vacuum where a hole in a wall will drain out the air. Burning flames inside a cabin using up all the oxygen and create fumes that cause damage and kill organic enemy unit and the player themselves. Damage the thermal control and decrease/increase the temperature within and use that up to the player's own creativity (freezing enemy in solid ice, boil them alive. Causing machinery to overheat or overclock). I guess other forumers could add a few suggestions of their own...traps and defense system...somehow that really reminds me of Dungeon Keeper II.... This would provide a lot more sidequest options which is instead of defeating the ship which should be made very hard so that players maybe would just sneak into ships doing stuff like stealing supply or tech from enemy ship, rescuing prisoner/alien creature, assassination, etc before sneaking out...in addition you can't mine through a ship main structure to avoid cheating (although the hull may or may not be breached or damage only by huge explosive which may kill the player themselves) maybe by making a ship main structure unmineable except by special equipment/explosive...lightsabers anyone? Finally just an afterthought if you got the option to mine/salvage defeated ships you could also create a small dungeonlike asteroid biome to be mined. Possibly would require special equipments, life support and suit/vehicles, protection against radioactive (similar to mining hellstone in terraria) to do it. In addition this could provide more options for sidequests for example monster infestation like in DOOM. Well, just a thought...Starbound is still great with what it already got...just a suggestion from people like me who's still nostalgic of the old classics like The Master of Orion and X-Com Apocalypse....
I think i've already mentioned something like this a while back, but yeah, it's a good idea and i'd love it to be implemented