I think that would be extremely difficult to and very limiting, especially with Assassin's Creed. The historical aspect means everything is already somewhat confined and the existence of the narrative created by the games limits it even further. Then once a certain era passes you can never go back to it again, which is all well and good if you're taking something beyond events of a world such as Lord of the Rings or Star Wars, but is awkward to pull off if you're wanting to have the same historical theme to things.
This isn't to say it can't be done, but it would have to ditch the categorized eras in place of something much more fluid in a completely different section. It would be interesting for character applications to, in addition to the first character, have a section for their bloodline as the timeline moves along and you take on the role of their descendants. But again, something like that would be complicated to pull off and would need serious, dedicated writers.