1a alternative having goner/Argon constantly friendly because of jumpdrive and
3. storage stations for stations (you probably wants your HQ at secure location, not on some new sector where you building your new complexes), especially such station important because you cant transfer stations between TL ships (only through your HQ), obviously they would be used for build soft mk3.
4. build soft mk3 should be able to update your complex (add new factories, upgrade SELECTED factories) without rebuilding it, if it cannot do it because of space constrain it should ask player permission for rebuild, probably should have cheaper light version with limitation on how many stations and how many mines, now it's very late game feature because of its cost.
5. system override software working as in xrm (i.e. using hackerchips, blueprint for them could be sold through Explorers guild), actually there are two different system override software in x3FL now (one duke's; one pirate's) may be they should behave differently and cost differently and named differently.
6. build able jump beacon even if it will cost a lot and be killed in non player sectors.
7. ability marines teleport from space to ship (some sort of marine auto collect software) range may be less than standard teleport range, but i hope for 3km at least, and bulk teleport marines from ship to ship. (mod that did work in AP does not work in FL for marines).
8. ability change weapons in bulk on ships (i.e. change all front guns from point-singu to beam), even if this would be slow.
9. new very hard military aldrin plot (against xenon).
10. software for fast flush cargo between transports (for Ozias & many docked to him transports), i.e. free this transport (all cargo would be transferred to other docked transports, should respect specified reserve batteries for jump, and does not move installed equipment (weapons, shields...) ), may be same should work if docked to station too (then it moves to station first, and only after that to other docked TRANSPORT ships doing nothing), and reverse for specified ware.
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11. memorial for marines who lost their lives (and reason of their life lost i.e. did they died in space, burned by shield, or in combat, or by final check before hacking on xenon ship).
at very list message to log is needed (with their final stats).