[Suicide Junkie]

I'd add to that gameplay list:
- Damage pattern option in damagetypes.txt (directional vs radial vs slices vs hitpoint-lottery vs slot-lottery vs size-lottery)
- Formula to choose the ship experience type in vehiclesizes.txt (Normal vs berzerkers->all attack bonuses vs monster digestion->eating ships generates resources)
- Recalculate component/design abilities on game load option in settings.txt
- Number of decks option in settings.txt

The first one would allow me to work up an interesting combat system to rival SE4.

The second two would allow for awesome monsters that grow over time and need to eat enemy ships in order to spread. Larvae would be completely invisible without weapons, and creep around to infest player systems, then slowly lose their cloak over time as they grow weapon damage as adolescents 15 turns later. They would then attack ships to fill up their bellies and pay maintenance on the next generation of monsters.
Adult monsters at age 30 turns would have their weapons atrophy, but grow SY ability in order to spawn more larvae using the resources generated by their XP.