Capital ships. 4-5x the size of the current ships.
- Multiple gunnery stations - kind of like the boss has - each gunnery station could assists one gun. Could be expanded to multiple shield/droid/other stations, auxilliary bridge, etc.
- New types of stations - this has been discussed elsewhere, but things like EWar and such. Good examples here - viewtopic.php?f=4&t=2033
- Tasking crew members to specific tasks (imagine Dwarf Fortress, but very simplified) - having a few Rockmen running around as a fire crew automatically fighting fires on a huge ship would help, as would a small team of Mantis to repel intruders. A repair team of Engis could run around repairing systems. Each team could require power for the same pool (1 power per 2 team members) so you'd have to juggle your teams or even choose to leave some out completely.
- Installing extra floor hatches to empty a room of O2 that are not on the edge of the ship (could be very expensive)
- Installing automated defenses (floor turrets, etc)
- Manned fighters alongside drones - more expensive than drones, new 'subsystem' (Hangar) - Pilots would gain experience for fighting, and obviously could be lost in battle. Would require crew members to maintain and repair ships as well as a tac comm center.
- Different mission than running from Rebels - maybe invading their homespace instead, with some sort of ticking clock as well. Gets tougher the closer you get to their HQ.
- If fighting normal sized ship, multiples of the enemy ships would be interesting - 2 or 3 of them versus you. You'd have to prioritize and focus fire, or try to simultaneously disable key systems.
The ships would be balanced, of course - one type of ship could lend itself towards being a carrier with multiple hangar bays available, another could be a gunship with loads and loads of gun slots and gunnery stations, etc. Jack of all trades could be even more difficult than it already is.
Something like this would be a major expansion of the game... and I'd gladly pay $15-$20 for it if it used the same mechanics FTL already has and built on them.
Just a long shot of a wish, but man... I'd be in heaven. More than I already am with FTL.