The game changes are:

Invert scroll direction setting
Added drag-and-place buildings, if you keep the mouse pressed the game will place the next building at the edge of the energy range from the previous one
Made it possible to select and sell multiple buildings at once, also added “getSelectedBuildings” Lua hook
Added an option for the defenses to hold fire
Shaded map edge
Map expansion marker line
Double-size minimap for resolutions larger than 800×600
Changed damage calculation of missile turrets
Removed the age limit of solar plants
Removed the boss aliens
Energy links will attempt to avoid sending energy to links that are pointing towards itself
Made it possible to change language setting in the settings menu
Changed so that Poseidon and Ares are unlocked by gaining award points

And we’ve also changed a bunch of stuff in the engine:

Replaced the standard Lua intepreter with LuaJIT2
Replaced BASS with OpenAL for sound effects
Made profiles and save games “Program Files safe” (see more below)