The addition of new maps, random map generator, and most of all, all the new nations. The game is basically the same (although it undergoes iterations all the time... as it always has), but the amount of content has expanded greatly.
I never played dom 2 or 3, but even in dom 3 itself there have been many advances in modding and unit limits, and many additional nations. So I would say probably the biggest advances have been made to the number of options you have available to you as a player, as to how you can play the game.