Perhaps all of my suggestions have already been made, but at least I might support one of these ideas to give it an additional push. ;-)
New Game Mode: Privateer
What about a game for being a freelancer? You might go where ever you want to, take jobs from different guys and try to get up your existence (and of course your ship).
This needs a feature like random events and quests, but as this is your own engine, there are plenty of possibilities to prevent a quest build like go t A, battle B and get back to C.
Trade missions, secret missions or transport missions are just a very small glimps of it possibilities.
For this, one might need additional rooms perhaps a sickbay, cargoroom, perhaps a shuttlebay (for cargoshuttles or even smaller fighter), for this something like an industry section would be nice, which produces "material" you need to rebuild lost shuttles (nothing else than the ammunition mechanics), guest quarters, VIP rooms, airlocks (for not having a shuttlebay).
Internal transportation system
I've read about a transportation system like beaming for internal transport. Some kind of conveyor belts are already implemented, but what about a lift system? Crew might enter the lift system and get off at another position. It might be faster than conveyor belts, but slower (and not that energy consuming) than teleporters. ;-)
Diseases
It might be very cool, to have diseases on board, perhaps while discovering a new planet or something like that. Star Trek Fans will know, that the most dangerous places on board a ship is in front of a console while being in battle. ;-) So incoming damage might hurt crewmen how may than head to sickbay to get healed. (New room: Sickbay, but I've mentioned it before)
Railguns
For the fast firing method. Railguns in different version might go from a fast Point Defence to a big and low Long Range Artillery.
Oxygen
When loosing rooms in battle it might be nice to loose atmosphere as well. At a certain amount of low oxygen crew gets slower until no oxygen (the die). It is an additional target to aim for instead of only reactors. ;-)
Stations
Yep, I often read about them, but they need not be at first priority. ;-)
But they might upper the game to a new level. If stations find their way into the game, it could quickly get to a level like X3, with players having their own industry empire (with mining stations, traderoutes to industry stations, etc...). This again might be part of the privateer mode and the presence of transports opens the possibility of being a pirate, etc...
But this is a very huge project! Perhaps a part for modders, if the engine allows those developments?
Full shields
I'd like to have a shield system for the whole ship (with less hitpoints, but generally defending every part). On critical sections this general shield might get assistance by normal shields.
Variant shields
The normal shields have a a shielding arc in front of them. Is it possible to alter the distance the arc has from its base? This way it might be possible to build overlapping but energy intense shield segments for important areas. ;-)
specialised shielding
What about shields who are better against one kind of damage than others?
natural surroundings
Like asteroid fields (ramming your ship/shields), solar flares (causing fires in unshielded areas), black holes (drawing you to the event horizon), nebulas (low sensor range, unable to target enemy subsystems, causing damage on hull or allowing ship to hide behind thicker parts of nebula clouds)
Cloaking devices
It might be a nice feature to hide a ship (or in case of bigger ships parts of the ship) in battle or during (privateer mode) certain missions.
A cloaking device might use a incredible amount of power and does not allow to fire weapons while cloaked. A generator hides everything inside its range. Larger ships might therefor need more than one generator.
Internal fights (boarding)
All though I'd like the idea of entering enemy ships and adding that ship to my fleet, I think this additional level of battles is not needed for this game. ;-) On the other hand, it might be appropriate to enter a ship, after you have destroyed the enemy oxygen system and the crew has died. I think if this feature will ever be added to the game, is a question best solved by an option selected at the start of the game.
