It changes more than I can list here. New weapons for units and carrier, the ability to automate production based on your target stock levels, manually controllable and re-dockable scout drone, ability for the scout drone to detect nearby targets and display a list on the side of the screen, enemy island difficulty settings, re-spawnable enemy carrier in strategy mode, improved controls of units, flexible refuel and repair of units, various measures to prevent and alert to stuck Walruses, improved radar showing the island terrain, improved camera angles and adjustable field of view, timed auto-saves and automatic backup of saves to name some of the bigger features.
Check the screenshots, especially the customization menu to get an idea of some of the things that can be adjusted.
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