Great ideas coming in, I have added some of them to my list in #2 post.
I like the idea of centering around a Ancient Israel mod also, but what would we considered ancient Israel? Up until the destruction of the second Temple?
I do think that modern Israel elements should be included so that more changes could have an effect as the game progresses in time.
Jewish semi-autonomy continued long after the Temple was destroyed. I would probably extend what I consider "Ancient Israel" at least until the time of Yehuda HaNasi, and possibly up until the dissolution of the Sanhedrin in the early 5th Century. In practical terms, I'm not sure what that would mean -- other than including Tzippori as a city.