Having just finished the course but not experimented or customized anything yet; off the top of my head I would probably suggest:
- Customizable squad/units with different equipment, skills/talents, stats.
- More advanced Interactables; keys for doors, consoles to hack doors or something else, traps
- Better more subtle AI: where Stealth/Awareness or melee fighting; actions based on Unit type: heavy, sniper, CQC expert; Patrol path, Searching due to alertness
- Actions, Effects, and Interactables that could affect and cause different effects: napalm grenade that causes patches of fire or catch a crate or unit on fire and do Damage over Time.
- Fog of War