There are certain things that are hard-coded, mainly for performance reasons and the extra difficulty involved in making them more flexible.
Things that you can currently mod in the game:
- Global defines
- AI personality
- Asteroid belt configurations
- Asteroid graphics
- Asteroid mineral variants
- Colony and planet infrastructure graphics
- Faction colors
- Jumpgate graphics
- Particle visual effects
- Planetary bonuses
- Planet types
- Races
- Factions
- Faction leader names
- Research
- Ships
- Ship formations and bonuses
- Ship modules
- Ship engine and trail colors
- Galaxy background/star colors
- Sector background colors
- Sector/planet names
- Trade resources
- Leader traits
- Turret and hardpoint graphics
- User interface color schemes
- Audio
- User interface layout and graphics
- Ship and faction AI
- The games base resources (metals, credits, food, crew, troops and research data)
- Galaxy generation algorithms