Well how could you bring another group into the Ark that isn't evil?
hmmm... I guess you could have the Ark crash into a land mass, Tibet maybe? The land mass is home to many refugees, what was once a series of remote villages and monasteries are now developed into large settlements and connected by make shift bridges. The arrival of the Ark was a huge surprise, though whether it was pleasant is debatable. The Ark once again establishes connection with humanity. The majority of Arkers (made up word here but what are they supposed to be called?) wish to take this chance to repair and rebuild the damaged Ark into the sustainable floating city it once was using the resources available to in the mountains. Upon completing these repairs they would once again set sail, remaining in contact with the land mass, in hopes of finding other land masses for remnants of humanity and/or resources. The majority of the Landdwellers want to take the Ark apart, and using its advanced technology to improve the settlements so that the settlements can run more sustainablly. They argue that the rest of the world is almost certainly underwater (Tibet being the highest place in the world, if i'm not mistaken) and don't want to give precious resources to the Ark for what seems like a wild goose chase. The Arkers believe that the seismic activity (they are scientists after all) during the flooding could very well have raised aother landmasses higher than even mt everest (i watched 2012, sue me), and that the Ark can be used as a medium to unite the rest of humanity. Of course neither are willing to back down which results to extremists emerging as the months drag on. While officially the two sides are still in the middle of a diplomatic solution, civil war is begining to emerge over the horizon of the endless ocean...
I would love to have a map where the Ark crashes, leaving shards of steel to penetrate the mountain side. Or an old Tibetan monestry which has been partially modified into a generator supplying power to one of the biggest settlements on the land mass. Or a system of caves which have been developed into a shanty town.
and horse you are right about that, but this thread is more about what would happen in the story of the sequel, rather than gameplay. of course we all hope all those you mentioned would be included in the future, whether as expansion, DLC or a sequel.