Galactic Civilizations II: Dark Avatar

Galactic Civilizations II: Dark Avatar makes enough changes to qualify as a full-fledged expansion, though you could be forgiven for not noticing most of them immediately. The new races aren't that much different from the old ones, the asteroid mining is a minor asset to your industrial sector and many won't play the new story based campaign for very long. But developer Stardock shows that if you add enough tweaks, you can force even veteran players to rethink their entire approach.

Rethinking is not the same as rediscovering. Just like the original game, your first move will still be exploration and spamming colonies to grab all the best planets as soon as you can. But now you can settle planets that would normally be off limits - if you research the right techs. So you can settle that water planet, but you will need to divert your science away from the usual military or economic tech. This early choice can set the tone of your game in dramatic ways.