Ok here are some thoughts on what the time era could be.
I'm going to mostly keep it 1500 onwards as I would think that the game would want a link to the modern day so you would probably encounter firearms.
Modern Times: The game would almost certainly be partially set in the Modern times as Juno is lose and ACIII had some proper missions set in the present day.
American Civil War: This would be an interesting time to cover for the political and moral issues of the time but I imagine they would want it to be a less predictable period and in a different country.
Pre-Stone Age: They could do it in the time of "those who came before" but I highly doubt this would happen yet as it would be much harder to design than a modern era game would.
World War One: While plenty of us know about WWI it has become somewhat overshadowed by WWII and they could cover many parts of it that we didn't know.
England post Henry VIII: After Henry VIII's death there was much conflict of who succeeds him due to the frailty of his son Edward VI and the disputes between Protestants and Catholics that had been caused by Henry's reign due to him turning England into a protestant country and the Catholics wanting it to become a catholic one again.
China in the 1500s: Following Shao Jun or an Assassin she worked with would be interesting and would provide a good change of gameplay that wouldn't be too dissimilar from previous games and you could continue to use the rope dart.
Napoleonic Wars: A conflict between the British and French Empires with so many other countries involved has plenty of potential for an Assassin and Templar story.
Do you guys have any ideas?