Major changes include multiple improvements to make the game more playable. The game now has space monsters, neutral natives on planets, and a very basic ground combat system for capturing planets. A lot of little balancing tweaks were also made to enhance playability. New building and binary star variant star graphics. New sitrep messages. The game will now ignore old config.xml files, preventing some crashes after updating.
The full screen turn progress window has been removed and the map now stays visible between turns. An encyclopedia has been added to the in-game interface, which shows information about game content like ship parts, techs, species, etc. Multiplayer games can now have AI and observer players. It is now also possible to have AI only multiplayer games with a human observer.
Scriptable species definitions were included. Planets now only have a single focus selection. There are new meter types for max and target meters, etc.