That's a great idea!
So if I had a clue about how to make a mod, I would definitely make a new faction and give it a name. Give them a hideout, kinda how the DB has their DB sanctuary. Make it hard to join them, like you can't just walk up to their hideout and knock on the door and join. Either they have to find you, or maybe you have to have certain skills at a certain level requirement. Definitely have a new set of armor, maybe different variations of it. Like the guy in charge will be wearing the same armor as his members, but maybe a different color variation to signify his significance. I would also make weapons to match the armor as well, at least a bow, sword, and dagger. Maybe create a couple books about them and scatter them around Skyrim.
I don't think you have to strictly stick to Assassin's Creed dynamics (like go through all the trouble of making a group as the Templars and have the whole Animus and technology thing either). Maybe in the books you could explain the story of how they were against another faction, like the Templars, in history. But now they have come to Skyrim and the other faction is no longer a threat.
If you could, give some dialogue to the guards that recognize your status within the faction. Kinda how the guards say, "Psst I know who you are, hail sithis!" if you're with the DB. Not sure how hard that would be as I only download mods, have never made one myself.
Another cool thing would be if you had a special horse, kidna like the Shadowmere concept, and put armor on it that matches the colors of the faction's unique armor. The horse could be white and fitted out in silver armor to represent the guild's good intentions, unlike how Shadowmere is black with red eyes. Give it superior stats like Shadowmere has.
You could also create a few new conjuration spells, like summon an old assassin that will fight with you. Or maybe an invisibility spell that does NOT break when you open things or toggle things or cast a new spell, unless there already is one and I just don't know about it.
That's all I can think of at the moment!