A lengthy piece on Polygon details the process. For starters, the team is handed a number of new civilizations by the production team, which determines it by how much bandwidth it has to create new art. It chose nine for Brave New World, in part to match the number from the last expansion, Gods and Kings.
Then it came down to determining which countries would make up those nine. Part of it came from noting what's underrepresented. It looked at the community to determine these, and came up with Indonesia, Brazil, Zulu, and Morocco. Three of those four are from South America and Africa, which Firaxis had already decided needed more representation.
After that, choosing the other five came down to deciding which countries fit with its design goals, or what could add new twists. Portugal and Venice were natural fits for the new trading system, and Poland's social policies worked well with the revised policy system. Assyria was a unique mix of science and expansionism, while the Shoshone allowed a more peaceful game based on a defensive bonus.
Check out the full piece for more details. Brave New World is due out on July 9.