A change of the religion of the Assassins should be good. They were Muslim, not Zoroastrian. Also, to my understanding the Assassin faction is different than the existing Hashashin order, even though historically they were the same thing.

Actually the Ubisoft Assassins were not religious mostly as they began to find out more about the First Civilization. I think a cynical modifier or a secular religious modifier should be added

If I may make suggestions, I think mod would be improved if the missions were less repetititve.

Maybe after you join the Templars or Assassins you get prestige and society points by killing members of the enemy order (whether by murder plots or by executions), while randomly recieving missions (just like in the other societies). Then to increase prestige and society points you should be able to pick a "hunt assassin/hunt templar". And in these missions you should be hunting actual characters from the other side.

I also think there should be some interpersonal decisions and events. For instance maybe you are an Assassin and your friend or lover or relative is a Templar (or vice versa); there could be an event to try and convince them to defect to your side (with sucess depending on their opinion of you and your diplomacy, and with failure carrying the risk of that person becoming your rival). Another event could be where if one of a character's parents gets killed by a member of one side, that character joins the other side immedeatly and becomes a rival of their parent's killer.

Would it be possible if maybe you added new pieces of Eden across the map, hidden blade artifacts that boost assassination plots. And what I think would be cool (along with the stuff Das Boot said) would be adding multiple brotherhood across the map with their own mentors, assassins, and logos like the Italian Brotherhood, Levantine Brotherhood, French Brotherhood, etc...