- Instantly unlocking all characters is now an option under the "Universe" tab if you weren't enjoying discovering them (and they also unlock quicker in normal play anyway).
- You can access your star character in the editor at any time (with realistic limitations at first).
- The criteria for editing powers/stats has been reduced to just eliminating one side instead of zombies as well (although you remain strongly advised to let the game play out naturally at least once).
- "Reincarnation" becomes available as a Universe option once zombies have had a chance to appear.
- You can now specify ANY of the game's 8 themes as a title theme under the "Audio" tab if you don’t like the default mix.
- New mysteries include finding a spy within your side and finding out who was behind the civil war.
- Mystery clues now include more references to their superhuman form (or lack thereof).
- You can ask a fellow superhuman to teach you one of their powers (with a low success rate).
- Completing missions for superhumans may inspire them to share their powers.
- Alternate versions of the "protégé" storyline allow you to become someone's double or have them become your double.
- "Interval" fight scenes no longer show the green "Fight!" text for each entrant.
- Super names are used in Fight Scene commentary where appropriate.
- When watching a fight scene, the meter & camera find somebody else to focus on upon elimination.
- Elaborate transformations like tunnelling aren't used unless you have enough spirit left to complete them.